Olive (Olea europaea L.) is one of the most economically important crop from east to the west around the world. The aim of this research was to investigate the genetic relationship among 41 olive genotypes, including 11 well-known Turkish cultivars and 30 Azerbaijani olive genotypes using simple sequence repeat (SSR) markers. In this study, 19 SSR markers were amplified 115 polymorphic SSR alleles. The number of polymorphic alleles ranged from 3 to 10 with an average of 6.05. The observed heterozygosity (Ho) varied from 0.05 to 0.93 with an average of 0.63 and expected heterozygosity (He) differed from 0.26 to 0.86 with an average of 0.72. The polymorphism information content (PIC) ranged from 0.23 to 0.85 with a mean of 0.68. A UPGMA cluster analysis grouped olive genotypes into two distinct clusters and both clusters were divided into two subgroups. Similarly, STRUCTURE analysis assigned olive genotypes into two different gene pools (K = 2) and four gene pools were identified representing the two subgroups by STRUCTURE analysis for K = 4. The genetic similarity of olive genotypes ranged from 0.36 to 0.95. These results revealed that there was a high genetic variation among 30 Azerbaijani olive genotypes. 'Ayvalik 1'and 'Ayvalik 2' from Azerbaijani olive genotypes were different from Turkish local olive cultivar, "Ayvalik" indicating homonymy. This research also highlighted that Azerbaijani olive genotypes were totally distinct from Turkish olive cultivars demonstrating that these olive genotypes might have been imported to Azerbaijan from different countries other than Turkey. The outcomes of this study indicated that these diverse olive genotypes could be useful for development of new olive varieties in Azerbaijan and future breeding programs between two countries could be enhanced by means of these results.