Top 10 eDNA Startups Revolutionizing Biodiversity Monitoring in 2025

Last updated: March 8, 2025 | 9 minute read

The world beneath our waters remains largely mysterious, with countless species still undiscovered. Meanwhile, on land, tracking endangered species has traditionally required invasive trapping or time-consuming field surveys. But what if we could detect animals just from the DNA they leave behind?

This isn't science fiction. Environmental DNA (eDNA) technology is transforming how we monitor biodiversity by analyzing the genetic material organisms shed into their surroundings. Rather than spending weeks searching for elusive creatures, researchers can now collect water or soil samples and identify dozens of species from a single test.

We've been following this field since its early days, and the recent innovations by startups in this space have been nothing short of revolutionary. These companies aren't just developing incremental improvements—they're fundamentally changing our ability to understand and protect the natural world.

What Makes eDNA Technology So Powerful?

Environmental DNA refers to genetic material collected from environmental samples rather than directly from organisms. Every living thing—from microscopic bacteria to blue whales—constantly sheds DNA into their environment through skin cells, mucus, waste, or reproductive materials.

Modern sequencing technology can detect even trace amounts of this genetic material, allowing scientists to identify which species have recently been present in an area. A single water sample might contain DNA from dozens of fish species, while a soil sample could reveal everything from earthworms to elusive mammals that passed by days earlier.

The applications seem endless. Conservation groups use eDNA to monitor endangered species without disturbing them. Environmental regulators detect invasive species before they become established. Fisheries managers assess populations without harvesting fish. Even public health officials track disease-carrying organisms in water systems.

What's changed in recent years is the accessibility of this technology. Advances in portable sequencing devices, simplified sample preparation, and powerful analysis algorithms have moved eDNA from specialized research labs into the hands of field biologists, citizen scientists, and commercial operations.

Top 10 eDNA Startups Changing the Game

Here are the companies making the biggest waves in environmental DNA monitoring and analysis.

1. NatureMetrics

Based in the UK, NatureMetrics has emerged as the clear leader in commercial eDNA services. Their technology transforms environmental samples into detailed biodiversity data through a combination of advanced DNA extraction techniques and proprietary analysis pipelines.

What sets them apart is their end-to-end approach—providing everything from sampling kits to final reports interpreting the data. Their systems can process environmental DNA from freshwater, marine, and terrestrial ecosystems, detecting thousands of species from bacteria to mammals.

"Traditional biodiversity surveys miss a huge proportion of what's actually there," a conservation biologist told us after comparing NatureMetrics' results with conventional methods. "Their eDNA approach revealed nearly twice as many vertebrate species as our standard monitoring protocols."

The company recently secured significant funding to scale their operations globally, partnering with major conservation organizations and government agencies. Their technology has already been deployed in over 80 countries to monitor ecosystems ranging from tropical rivers to Arctic tundra.

2. Jonah

Swiss-American startup Jonah has taken a unique approach to eDNA by focusing on automated collection systems that continuously monitor aquatic environments. Their solar-powered floating platforms can filter water and preserve DNA samples for weeks without human intervention.

This continuous monitoring capability represents a significant advance over traditional point-in-time sampling. By tracking how DNA signatures change over days, weeks, and seasons, Jonah's systems can detect early warning signs of ecosystem shifts or invasive species arrivals.

Their newest platform incorporates onboard DNA extraction and analysis, transmitting results in near real-time to environmental managers. This capability has proven particularly valuable for early detection of harmful algal blooms and invasive mussels in municipal water systems.

"It's like having a 24/7 biological security system for our water resources," according to a water utility manager using their technology in the Great Lakes region.

3. VigiDNA

French startup VigiDNA specializes in marine eDNA monitoring, developing technologies specifically optimized for the challenges of ocean environments. Their sampling systems can be deployed on everything from small research vessels to autonomous underwater vehicles, collecting and preserving eDNA at depths up to 1,000 meters.

Their breakthrough came with a preservation technology that stabilizes DNA in saltwater samples for up to three months at ambient temperatures—solving a major logistical challenge for remote marine research. This innovation has enabled biodiversity surveys in regions where maintaining cold chains for sample transport was previously impossible.

VigiDNA's systems have been particularly valuable for monitoring marine protected areas, where their non-invasive sampling provides comprehensive species inventories without disrupting sensitive habitats. The European Union recently adopted their technology as the standard method for biodiversity assessments in its Marine Strategy Framework Directive.

4. Biome Makers

While many eDNA companies focus on detecting animals and plants, California-based Biome Makers has specialized in analyzing the complex communities of microorganisms in soil. Their technology identifies thousands of bacteria and fungi species from soil samples, creating detailed maps of soil health.

Their flagship product, BeCrop, uses eDNA to assess agricultural soils, helping farmers understand the microbial communities supporting their crops. This information guides more sustainable farming practices—optimizing fertilizer use, reducing pesticide applications, and improving crop resilience.

"After decades of treating soil like dirt, we're finally understanding it as a living ecosystem," a regenerative agriculture consultant told us. "Biome Makers' technology gives farmers a window into the invisible workforce beneath their feet."

The company has analyzed over 200,000 soil samples across 35 countries, building what may be the world's largest database of soil microbiome information. This dataset is becoming increasingly valuable for climate research, as soil microbes play crucial roles in carbon sequestration.

5. Revive & Restore

While not exclusively an eDNA company, the nonprofit Revive & Restore has pioneered innovative applications of environmental DNA for conservation. Their "Genetic Rescue" programs use advanced genomic techniques to protect endangered species and even explore de-extinction possibilities.

Their eDNA initiatives focus on detecting extremely rare or potentially extinct species that evade conventional surveys. By developing highly sensitive assays targeted to specific endangered species, they've helped confirm the continued existence of animals thought possibly extinct.

In a high-profile success, their eDNA techniques detected traces of the nearly extinct vaquita porpoise in the Gulf of California, providing crucial data to conservation efforts when traditional sighting surveys found none. Similar approaches are being applied to search for other critically endangered species around the world.

Beyond detection, Revive & Restore is exploring how eDNA can inform genetic rescue efforts by revealing population structures and genetic diversity from non-invasive samples—critical information for conservation breeding programs.

6. Trace Genomics

Combining eDNA technology with machine learning, California-based Trace Genomics has developed sophisticated systems for analyzing soil microbiomes in agricultural settings. Their soil tests identify pathogens, beneficial organisms, and overall microbial diversity from DNA extracted from soil samples.

What distinguishes their approach is the integration of massive datasets with advanced AI to interpret the results. Their systems can predict crop disease risks, evaluate the effectiveness of soil treatments, and recommend management practices based on the genetic fingerprint of a soil sample.

The company recently expanded beyond agriculture into environmental restoration, helping land managers assess soil health for reforestation and ecosystem rehabilitation projects. Their technology provides crucial benchmarks for measuring the biological recovery of degraded lands.

"Conventional soil tests just look at chemistry," explained an environmental consultant working on mine reclamation. "Trace Genomics shows us whether the soil ecosystem is actually coming back to life."

7. Ande

Massachusetts-based Ande has focused on making eDNA technology more accessible through portable, field-ready DNA analysis systems. Their Rapid DNA platform can process environmental samples and generate species identification results in under two hours—all with equipment that fits in a rugged suitcase.

This portability has proven transformative for fieldwork in remote locations where sending samples to centralized laboratories is impractical. Conservationists working in tropical forests, for instance, can collect water samples in the morning and have detailed species inventories by afternoon, allowing them to adjust their survey efforts in real-time.

The system has found particular application in biosecurity, where rapid identification of invasive species at ports and border crossings can prevent environmental disasters. Customs agencies in several countries now use Ande's technology to screen ballast water from ships and soil from imported plants.

8. BaseClear

Dutch biotechnology company BaseClear has leveraged its deep expertise in genomics to develop specialized eDNA services for environmental monitoring. Their metagenomics approach goes beyond simple species identification to analyze entire ecological communities and their functions.

Their environmental genomics division specializes in complex samples like wastewater, harbor sediments, and industrial biofilms—environments where traditional monitoring techniques struggle. Their analysis can identify thousands of microorganisms while also detecting antimicrobial resistance genes and pollution indicators.

European regulatory agencies have increasingly adopted BaseClear's methods for water quality assessment, as their genomic approaches provide more comprehensive information than conventional microbiological testing. Their technology has been particularly valuable for monitoring the biological impacts of offshore energy developments in the North Sea.

9. DNASense

Danish startup DNASense has pioneered the application of eDNA technology to industrial systems and built environments. While many companies focus on natural ecosystems, DNASense analyzes the microbiomes of wastewater treatment plants, brewing facilities, hospitals, and other engineered systems.

Their approach has proven particularly valuable for troubleshooting biological processes in industrial settings. When a wastewater treatment plant experiences problems, their eDNA analysis can identify exactly which microbial populations are thriving or declining, guiding interventions far more precisely than traditional methods.

The company recently launched a building monitoring service that uses eDNA to assess indoor environmental quality, identifying potential pathogens and allergens from surface and air samples. This application has gained significant traction in healthcare facilities looking to prevent hospital-acquired infections.

10. DiveBioSciences

Australian startup DiveBioSciences focuses specifically on marine eDNA technologies for coral reef conservation and fisheries management. Their specialized collection methods and analysis pipelines are optimized for the unique challenges of tropical marine environments.

Their innovations include autonomous underwater vehicles equipped with eDNA collection systems that can map biodiversity across reef systems without human divers. These surveys have revealed surprising patterns of fish distribution and helped identify priority areas for conservation.

For fisheries applications, their technology can assess fish stock abundances from water samples, providing a less disruptive alternative to traditional net surveys. Several Pacific island nations have adopted their methods for monitoring both commercial fish stocks and the effectiveness of marine protected areas.

"We used to understand so little about what was happening on our reefs," a marine park manager told us. "DiveBioSciences' eDNA surveys give us the equivalent of thousands of diver observations from just a few water samples."

The Future of eDNA Technology

As we follow developments in this field, several trends are becoming clear. First, integration with other technologies—particularly autonomous collection platforms and artificial intelligence—is rapidly expanding what's possible with eDNA. Second, standardization efforts are improving data comparability across different studies and regions. Finally, costs continue to fall while sensitivity improves.

Perhaps most exciting is how eDNA technology is democratizing biodiversity monitoring. Tools that were once available only to specialized research labs are increasingly accessible to conservation groups, citizen scientists, and natural resource managers with limited budgets.

As one conservation biologist put it to us: "eDNA is giving us a superpower—the ability to detect life we can't see, hear, or trap. It's like suddenly gaining access to a whole new sense."

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