Environmental DNA (eDNA) is DNA that is collected from a wide variety of environmental samples such as soil, water, or even air rather than directly sampled from a single organism. As organisms interact with their environment they shed DNA and it accumulates in their surroundings. In the last 8 years, advanced next-generation DNA sequencing technologies have led to the development of metagenomics: a method for rapidly measuring and monitoring biodiversity by sequencing eDNA and comparing it to curated databases of DNA sequence where the species are known.

Metabarcoding has many applications and can be applied to populations of bacteria, fungi (including airborne spores), invertebrates, plants (e.g. pollen), fish and even mammal detection. It can be applied to many environments such as freshwater, seawater, soil, sediments and other environments where sampling can be problematic. For example, say you wanted a list of the fish species present in a reservoir; eDNA sampling with metabarcoding could provide such a list more cost-effectively than gillnetting. The method is also appropriate for invertebrate surveys from pitfall traps, however, it is not a quantitative technique due to varying sizes of the organisms sampled.