Background The genetic diversity and structure of 31 popcorn accessions of the germplasm bank of the State University of Maringá were assessed using 30 microsatellite primers. Results 127 alleles were identified from 30 evaluated loci. The number of alleles per locus ranged from two to eight. The overall mean of the polymorphic loci averaged 79.89%. The primers UMC1549 and UMC1072 detected polymorphism in all accessions analyzed. The mean observed heterozygosity ranged from 0.07 to 0.30 and the highest proportion of heterozygous plants was observed in accession BOZM 260 (Ho = 0.30). The analysis of molecular variance revealed that 60% of the total genetic variation was found within accessions and 40% was found between accessions. The Bayesian clustering approach grouped the 31 accessions into two genetically differentiated clusters. The dendrogram revealed that accessions TATU 2 and ARZM 05 083 are genetically less similar than the others. Conclusions The analysis allowed to identify microsatellite loci with high levels of heterozygosity (UMC1549 and UMC1072). These loci can be indicated as promising for detecting polymorphisms in popcorn accessions and in the monitoring of genetic improvement programs. Moreover, allowed to identify heterozygous accessions (BOZM 260), this accession showed allelic variation at all analyzed microsatellite loci and can be recommended for crosses with plants that have desirable agronomic characteristics, with a view to the broadening of the genetic base of popcorn accessions and developing new cultivars.