This study aimed a taxonomic survey on genus Cosmarium in five oligotrophic lagoons in the Federal District, Brazil: Lagoa Bonita, Lagoa Joaquim Medeiros, Lagoa do Cedro, Lagoa Taquara and Lagoa dos Gansos. Samples were realized between 2006 and 2009, by macrophytes squeezing and/or submerged substrates scraping; 18 samples were analyzed and deposited at the Herbarium of the University of Brasília. They were fixed in formalin solution (4%) and analized under 400× and 1000× magnification. Altogether 42 taxons were found. Among them, 30 are cited for the first time in the Federal District and probably eight for Brazil. Lagoa Bonita had the higher number of taxa (32), followed by Lagoa Joaquim Medeiros (19), Lagoa do Cedro (16), Lagoa dos Gansos (15) e Lagoa Taquara (9). Cosmarium pseudopyramidatum var. pseudopyramidatum Lundell was the most common taxon, present in 100% of the samples.