In this study, genetic diversity was evaluated for 40 landraces and improved rice genotypes by inter-simple sequence repeat (ISSR), IRAP (Inter-Retrotransposon Amplified) and REM (Retro transposon-Microsatellite AmplifiedPolymorphism) marker systems. Amplified productions of 20 primers indicated distinct and polymorphic bands among genotypes that produced a total of 309 bands and an average of 88.03% polymorphism. The average gene diversity, Shannon’s diversity index and polymorphism information content were 0.39, 0.57 and 0.35, respectively. UBC811 and UBC813 markers showed the highest genetic diversity indices which were 0.65 and 0.64, respectively. In order to determine the efficiency of the markers in polymorphism appearance, marker index (MI) and effective multiplex ratio (EMR) were calculated which based onTOS2+UBC811and TOS2+UBC826 markers with the highest MI and EMR value, had better efficiency, respectively. The dendrogram obtained using UPGMA method divided genotypes into six clusters. The most of local rice varieties including Hashemi, Alikazemi and Hassansaraiee located in cluster two whereas improved cultivars such as Khazar, Kadous and Gohar located in cluster three. Also, the results indicated that markers based on retrotransposon as REMAP have good potential for using in genetics and breeding researches in rice.