Common bean (Phaseolus vulgaris L.) is one of the most important crops in Nicaraguan agriculture. Bean production is carried out on small scale farms, where farmers generally lack key inputs. Seeds have been identified as the most critical input in bean production. For this reason, national seed program will be a priority during next ten years. Among the four main seed quality components, genetic component has been the least studied. The occurrence of offtype seeds and plants in the cultivar ‘INTA ROJO’ during seed production has hindered the seed certification process and questioned the genetic quality of the cultivars produced in Nicaragua. The present study aimed to compare the genetic composition of different seed categories in the cultivar ‘INTA ROJO’, and to confirm the genetic identity of offtype seeds and plants found in this cultivar. The genotype frequencies of fourty individuals were analyzed using ten microsatellite markers in the following seed categories: Breeder’s seed, foundation seed, registered seed and certified seed. The genotype frequencies were analyzed using Fisher’s exact test, where breeder’s seed was assigned as a reference population. Additionally, twenty offtype seeds and plants, among them the offtype seeds known as “frijol viterra” and “frijol rojo oscuro”, were contrasted with breeder’s seed through pairwise comparisons of genetic distances. The results suggest that changes in genotype frequencies take place during seed production and they are ascribed to the selection pressures caused by environmental differences among production regions and inadequate varietal depuration procedures during seed production. In addition, the offtypes denominated “frijol rojo oscuro” were identified as an unknown cultivar probably derived from natural segregations, mutations and out-crossing among bean seed lots, and in less degree from accidental seed mixtures. In contrast, “frijol viterra” was confirmed to be the same cultivar ‘INTA ROJO’. Its differences in seed weights were associated rather to environmental effects than to genotypic ones. The seed technology implications of these findings and further perspectives are discussed