Near complete 12S DNA reference library for the freshwater fish of French Guiana, northern Amazonian region

The limited availability of DNA reference libraries is a key limitation to developing biodiversity inventories using environmental DNA techniques. This dataset provides a 12S mitochondrial DNA reference library covering 88.92 % of the species of freshwater fish inhabiting French Guiana. It contains 1,557 references, covering 369 species distributed across 51 families. It also covers the intraspecific diversity of most of these species. DNA was extracted from 1,439 specimens collected during over 25 field expeditions. DNA collections from museum records were used to complement the data for a further 118 specimens. The sequences cover two widely used eDNA primers for fishes (Teleo1 and 12S-V5) enabling identification of most Guianese freshwater fish species using eDNA metabarcoding. Beyond French Guiana, the dataset covers 6.31% of Neotropical fish species, 23.05% of genera, and 56.04% of families, making it valuable for broader regional studies. This dataset provides a comprehensive and reliable DNA reference library for the Neotropical fish, filling an important biodiversity gap in a remote, biodiversity-rich region that is difficult to sample.