Practical applications of environmental DNA (eDNA) are in exponential expansion, especially for the assessment and monitoring of freshwater metazoans. Because eDNA sampling and analysis is non-invasive, it improves the detection of threatened, invasive and exploited species for which monitoring may be challenging. Species detection efforts using a combination of eDNA and qPCR have been highly successful and, as a result, their use in species monitoring is expanding rapidly. We developed qPCR primers and probes in order to monitor many invasive, threatened or exploited aquatic species as part of various monitoring eDNA projects in the province of Québec, Canada. Here, we present a total of 60 species-specific qPCR assays (including PCR protocols, primers and Taqman probes sequences) developed for the detection of 45 fishes, six amphibians, five reptiles, two molluscs and two crustaceans. These comprised nine and 27 species respectively listed as invasive and threatened in Eastern Canada. These resources should be of broad usefulness not only for monitoring studies based in Québec but throughout the geographic range of the targeted species in North America.

Mismatchs of the 60 species-specific developed primers and probes with respect to related species. Primers and probes are presented in alphabetical order.