The knowledge on diet composition of the freshwater mussel Diplodon enno (Ortmann) would aid in its culture and propagation allowing, this way, the replacement of natural endangered populations in Brazil. Microalgae are the main food source for captive mussels and unionids have displayed an ability to sort algae based on the cellular characteristics prior to ingestion. The main objective of the present work is to analyze the phytoplankton composition of the water from and of the gastrointestinal contents of the mussel D. enno, as an initial step for development of a suitable rearing diet. Therefore, water samples and bivalve specimens were collected from S. Francisco River, city of Paulo Afonso, Bahia, Brazil. The microalgal composition found in water and stomach/gut content samples was very diverse being represented by the following divisions: Cyanophyta, Chlorophyta, Dinophyta and Heterokontophyta (Diatoms). Concerning the relative abundance of microalgae divisions, it is possible to state, for the water and gastrointestinal contents, that Cyanophyta represents 15% and 14%, Chlorophyta 54% in both, Heterokontophyta 31% and 27% and Dinophyta 0% and 5%, respectively. According to the Brazilian CETESB criteria for phytoplankton species classification, 50% of Cyanophyta and 15% of Chlorophyta species observed in the water samples were classified as “very frequent”, as were 68% of Heterokontophyta and 33% of Chlorophyta species in the gut/stomach tract samples. Focusing at a species level, although in the water only Coelastrum sp. and Chroococcus sp. were observed in 100% and 75% of the samples, respectively, in the gastrointestinal tract the species Staurastrum sp., Aulacoseira sp., Scenedesmus sp. and Fragilaria crotonensis occurred in 80% to 100% of the samples. The present results showed that D. enno feeds not only on small chlorophytes microalgae, due to their convenient size that facilitates higher feeding rates, but also on large size diatoms, due to a possible nutritional advantage for the bivalves. Thus, a diet composed by large diatoms and small chlorophytes microalgae may be considered as the most reasonable for the maintenance of D. enno populations.