The great biodiversity of the Serra da Bodoquena is the result of years of biological evolution. A complex combination of natural factors allows aquatic plants, fish and invertebrates to coexist in absolutely crystalline water springs. Together, organisms form an intricate web of life, connecting a single-celled microalga with large river predators. For better knowledge of the biodiversity of microalgae, an important tool is the bioprospecting and study of novel species, avoiding as much as possible the introduction of exotic species. Thus, the aim of this work was bioprospecting microalgae species from Bonito, MS, Brazil, in order to obtain more information about the local microbial biodiversity. Freshwater samples were collected from two lakes of the municipality. The samples were plated in Basic Basal medium added of bacteriological agar. After plating, the samples were kept in a biochemical oxygen demand (BOD) oven at 25ºC with photoperiod for growth. After isolation of the obtained colonies, the identification of the species was carried out according to the morphological characteristics of cells. Despite the long periods for adaptation, seven microalgae taxa were successfully isolated from the samples collected, four at the genus level and three at the species level; one from the Trebouxiophyceae class, five from the Chlorophyceae class and one from the Bacillariophyceae class.