In this study, Simple Sequence Repeat markers (SSR) were used to investigate the genetic variation between 49 cumin ecotypes collected from 9 different provinces of Iran. SSR primers Elap1479, Elap040 and Elap1493 showed the highest (89%), while Elap1340 and Elap017 showed the lowest (56%) number of polymorphic bands. Polymorphism information content (PIC) values varied between 0.18 - 0.37. The highest and the lowest PIC value were obtained by Elap017 and Elap1340 (0.37) and Elap040, Elap1493 and Elap1479 (0.18), respectively. Cumin populations of Semnan and Northern-Khorasan showed the highest difference, whereas Kerman and Esfahan populations exhibited the lowest difference. The obtained dendrogram classified all cumin population into three clusters at similarity level of 0.71; the first group was Semnan and Southern-Khorasan populations, the second includes Fars, Kerman, Northern-Khorasan, Khorasan-Razavi, Esfahan, Golestan and the third class consisted of Yazd populations. Based on these clusters, Kerman and Northern-Khorasan showed the closet genetic background and may belong to the same ancestor. The genetic markers used in this study can provide impetus information for tagging of economic traits. It can be concluded that the variability in the Iranian cumin populations have potential important source for cumin breeding objectives.