Several studies have confirmed that popcorn (Zea mays L. var. everta) has a narrow genetic basis, which affects the quality of breeding programs. In this study, we present a genetic characterization of 420 individuals representing 28 popcorn populations from Brazilian germplasm banks. All individuals were genotyped using 11 microsatellite markers from the Maize Genetics and Genomics Database. A Bayesian clustering approach via Monte Carlo Markov chains was performed to examine the genetic differentiation (Fst values) among different clusters. The results indicate the existence of three distinct and strongly differentiated genetic groups (K = 3). Moreover, the Fst values (calculated among clusters) were significantly different according to Bayesian credible intervals of the posterior Fst values. The estimates of posterior mean (and 95% credible interval) of the Fst values were 0.086 (0.04-0.14), 0.49 (0.376-0.624) and 0.243 (0.173-0.324) for clusters 1, 2, and 3, respectively. Clusters 1 and 3 showed a high level of genetic diversity in terms of expected heterozygosity and number of alleles, indicating their potential for broadening the genetic basis of popcorn in future breeding programs. Additionally, the 11 microsatellites were informative and presented a suitable number of alleles for determining parameters related to genetic diversity and genetic structure. This information is important for increasing our knowledge regarding genetic relationships, for the identification of heterotic groups, and for developing strategies of gene introgression in popcorn.