Abstract Microcystis panniformis is a planktonic freshwater cyanobacterium that has become increasingly prevalent in tropical water bodies in Brazil. Recently, it has been shown that the strain BCCUSP100 is able to produce microcystins (MCs, especially, MC-LR and [Asp3]-MC-LR), which are toxins that can affect the health of humans and other animals. This study explores genetic diversity among 14 strains of M. panniformis isolated from 4 freshwater reservoirs in 2 different Brazilian regions (north-east and south-east). Initially, the strains were morphologically characterized, followed by DNA fingerprint analyses using HIP1 sequences. Few morphological variations were observed and sequences of HIP1 were abundant in all strains studied. Strains isolated from water bodies in the south-east showed more evident genetic variation. Our findings also indicated genetic variation and the presence of different genotypes both between and within populations. The presence of M. panniformis in two distinct groups empha...