The genetic diversity and structure of 31 popcorn accessions of the germplasm bank of the State University of Maringá were assessed using 30 SSR primers, which identified 127 alleles. The number of alleles per locus and accession 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, and can be indicated as promising for detecting polymorphisms in popcorn accessions and to monitor improvement programs. The mean observed heterozygosity ranged from 0.07 to 0.30 and the highest proportion of heterozygous plants was observed in accession BOZM 260 (H_o = 0.30). The analysis of molecular variance (AMOVA) revealed that 60% of the variation was found within accessions and 40% between accessions. The bayesian clustering method grouped the 31 accessions into two genetically differentiated clusters. The dendrogram obtained by UPGMA revealed that accessions TATU 2 and ARZM 05 083 are genetically less similar than the others.