Cassava is a crop of great importance in providing calories to people living in tropical regions, and is extremely important for the remaining indigenous communities and traditional farmers in Brazil. The objective of this study was to characterize the genetic diversity among accessions of cassava germplasm originated from different regions of Brazil. Seventeen primers were used to quantify the genetic variability of 82 genotypes of cassava (33 genotypes from the Amazon, 24 from Central-West, 18 from the Southeast, four from Southern region, and three commercial varieties). High genetic variability was observed among genotypes, and most of this diversity was concentrated within regions. Cluster analysis using the neighbor-joining method of structuring classified the accessions in two groups, according to the origin of the accessions. The first group was mainly composed by accessions from the Amazon and the second group by accessions from the other regions, with a few exceptions. The literature confirmed the existence of genetic differentiation among regional groups of cultivars, and this structure is also associated with the content of cyanogenic compounds present in plant roots. The structure may be associated with food preference of human groups, considering that for food security the Amazon Indians chose cassava with high concentrations of cyanogenic compounds, as it presents certain advantages over the protection against attack by herbivores.