Citrus plants are cultivated in the North and South of IRAN. Little is known about the genetic variability of Iranian cultivated citrus germplasm collection. Microsatellite or SSR (Simple Sequence Repeat) markers are co-dominant, multiallelic, highly polymorphic genetic markers and appropriate for genetic diversity studies. Citrus Cultivated since ancient times in its centre of origin in south eastern Asia, citrus production has spread over the centuries into most areas that have a suitable climate (Webber et al., 1967). Today citrus is one of the most widely cultivated fruit in the world, and most major production areas are far removed from the original areas. Different Citrus species widely grown in more than 50 countries in the world. World production is increasing and has reached 70 million tones, according to FAO (Orford et al., 1995).