Mentha is one of the most important genera of the Lamiaceae with a wide geographical distribution and considerable commercial importance. The general aim of this work was to group 34 accessions from four species of mint using ISSR molecular markers to select some accessions to estimate the potential cross-ability of mints valuable in breeding and phytochemical research. The reproductive characteristics including the type of flower, petal color, sepal and petal lengths, length of stamen and pistil as well as the number of free and living pollen grains in the anther were also studied to find out cross-ability patterns and the possible reproductive barriers. Analysis of molecular variance (AMOVA) among and within species showed more intra-specific variation (92.24%) in comparison with inter-species variation (7.76%). Results of cluster analysis based on ISSR data grouped the mint genotypes into five clusters. By this, the greatest genetic similarity was found between Ms12 from M. spicata and Ml29 from M. longifolia. The genotype Ms12 along with Ms22, the other genotype from M. spicata, were found to be male sterile due to stopped stamen development. These two had higher combining ability (seed set) when used as the female parent in intra-specific crosses and when crossed with M. longifolia compared to the other genotypes in diallel crosses. The highest number of hybrid seeds was obtained where Ml29 was crossed as the male parent with male sterile Ms12 as the female one. This high success rate of seed set in interspecific crosses between M. spicata and M. longifolia could be related to their genomic similarity confirmed by ISSR molecular data. Therefore, producing hybrid seeds and subsequent generations from crosses between these species, utilizing male sterility mechanism, can be a source of new genetic variation for mint.