We present the results of a taxonomic survey of the genus Micrasterias in the Metropolitan Region of Salvador (MRS), Bahia, northeastern Brazil during 2007–2010 and 2014–2015. A total of 275 phytoplanktonic and periphytic samples from 11 municipalities were analyzed. The samples were collected using a plankton net with 20 µm mesh or squeezed from macrophytes. Twenty-nine taxa were identified, which 20 have their geographic distributions expanded. Only M. pinnatifida was considered frequent, occurring in 9 municipalities, while we classified 21 species as rare in the study area. Our results emphasize the importance of the conservation of aquatic bodies in the MRS for the maintenance of biological diversity of desmids and other aquatic organisms.