Genetic diversity and clasification of indica and japonica for 109 accessions of rice from the Mediterranean Area were studied by SSR markers and morphological traits. The results showed that 80.73% and 77.98% of the accessions were clustered into japonica group based on the two approaches, respectively, which means that most of the accessions of rice genetic resources from the Mediterranean Area were japonica ecotype. 37 ones were selected from 109 accessions to evaluate the compatibility with indica and japonica. 75.68% of 37 accessions shown good compatibility to japonica.The Mediterranean rice has high genetic diversity with 3.84 average effective numbers of alleles (Ae) and 0.482 average Nei’s genetic diversity index (H). The level of genetic diversity of indica group is higher than japonica group with Nei’s genetic diversity index of 0.459 and 0.340, respectively. These results are useful for properly conserving and effectively using rice genetic resources from Mediterranean Area.