Abstract An undescribed diaptomid copepod probably belonging to a new Mastigodiaptomus species has been discovered and was very abundant in El Junco Lake (San Cristóbal Island, Ecuador) from 1966 until 2004. The species was not found in samples from 2007, 2008 or 2018. The loss of this key species from the lake coincides with the illegal introduction of Nile tilapia to El Junco Lake in 2005 and its subsequent eradication in 2008. The disappearance of this biogeographically and ecologically important copepod population may be explained by direct mechanisms of predation and competition, by a combination of both processes, and by indirect mechanisms linked to alterations in the lake ecosystem. The effects of fish eradication using rotenone may have contributed to the loss of the diaptomid population and to preventing its recovery. This article discusses the search for sources of propagules for recolonization and possible reintroduction scenarios and procedures.