|In this study, 35 popcorn inbred lines that belong to West Akdeniz Agricultural Research Institute (BATEM) and Black Sea Agricultural Research Institute (KTAE) were subjected to molecular analysis. 21 SSR primers were used to determine genetic distances among genotypes for molecular characterization. According to the unweighted pair group method with arithmetic mean (UPGMA) cluster analysis, popcorn inbred lines were divided in to 2 main and 5 sub-clusters. Similarity coefficient was changed between 0.44 and 0.95 among inbred lines. The nearest genetic similarity was detected between 9 and 28 number. On the other hand, 1 and 9 numbered lines were found to be the most distant relatives. The results of the study revealed a genetic variation in the popcorn inbred lines that belong to West Mediterranean Agricultural Research Institute and Black Sea Agricultural Research Institute.