This dataset describes primary biodiversity data pertaining to pelagic diversity from the Bay of Toliara, Madagascar. The data is assembled in the framework of a specialized training program for students from Madagascar and its surrounding region (Pole de Formation Spécialisee, Institut Halieutique et des Sciences de la Mer). Additional data will be added along the years. Pelagic samples are taken in the Bay of Toliara using two ships and Plankton nets. The georeferencing is done using a GPS onboard ships, and samples are taken inside the lagoon (in two seperate locations); as well as on the outer fringe of the coral reef. The taxonomic determination are done by the students using a local field guide, under the supervision of their accompanying professor. Students enter data in Darwincore spreadsheet templates as provided by GBIF.