Mint is one of the aromatic vegetables and medicinal plants of the family Lamiaceae. Wich has many species and hybrids. This study was conducted to evaluete the genetic variation within and among Persian mint species using ISSR markers and some morphological traits. For this 50 genotypes of mint including 39 genotypes from M. spicata species, 7 genotypes from M. longifolia species, 3 genotypes from M. piperita species and one from M. aquatic species were studied. According to the results obtained 22 ISSR primers produced polymorphic and clear banding pattern. Overall for 421 bands were amplified and the rate of polymorphism 98.71 precent(416 polymorphic bands). For data analysis, ISSR bands throughout the gel profile were scored as present(1), absent(0) or ambiguous(9). The NTSYSpc software was used to generate genetic similarity(GS) matrixes, create dendrogram and corresponding cophenetic matrix and calculate cophenetic correlation. Cluster analysis showed that M. longifolia was clearly clustered with M. spicata in a single group. Similarity coefficient using Nei method confirmed this evident. Degree of genetic similarity of %0.88 was determined based on jaccards similarity conefficient. Based on the results of ISSR molecular marker the species M. longifolia has more affinity to M. spicata has the Nei similarity coefficient show that the similarity between this two species is 86 percent. The possible reason for this similarity is that M. spicata has been possibly evolved from crosses between M. suaveolens and M. longifoila . Cluster analysis and principal component analysis grouped the mint genotypes into six cluster genotypes belonging to M. aquatica was separated from the three other species in cluster analysis. Analysis of molecular variance(AMOVA) showed higher variation within species(87.58) compared to the variation between species(12.48). The genetic variation between and within collection centers was studied using analysis of molecular variance(AMOVA). Five collection center of mint species including North, South, Central, West and East ver considerate . According to these results %1.86 of the total variation was observed between the centers and %98.14 of the variation was assigned between center. The highest genetic similarity between collection center was between central part and west and lowerst genetic similarity was between the south and central part. Cluster analysis constructed this on morphological characters grouped 50 genotypes of mints species into 3 group. Cophenetic coefficient between morphological and molecular clusters calculated and correlation were calculated using NTYSIS. The correlation coefficient of 0.005 showed that there is no correlation between molecular and morphological characters. Overall the results of ISSR molecular markers in combination with morphological data shows considerable variation between species of mint, which can be used in breeding program.