Chocó-Darien is an important biogeographic realm, as it is a terrestrial biodiversity hotspot and the southern limit of the Caribbean reefs. However, to date there are no compiled data on the reef fish assemblage of this region. We provide an updated checklist of marine fishes from the Chocó-Darien reef system (Colombia), with comments on their geographic distribution and conservation status. Peer-reviewed studies, unpublished data and in situ visual censuses were surveyed to compose this checklist. A total of 212 reef fish species across 57 families were compiled, eight of which had no previously published records, one of which (Trachinotus falcatus) is recorded for the first time. The most speciose families were Labridae (n = 21), Gobiidae (n = 18) and Serranidae (n = 17). Fourteen threatened species were recorded, including one critically endangered (Epinephelus striatus) and two endangered (Balistes vetula and Scarus coelestinus). This study contributes to fill the knowledge gaps on the reef fish diversity of the Caribbean southern limit and raises concern on the spread of the lionfish invasion into the Chocó-Darién reef system.