Six rice cultivars, Annapurna, Ramakrishna, TKM 6, Zenith, Tetep and Tadukan were evaluated for their resistance/ susceptibility reaction against four rice root-knot nematode (Meloidogyne graminicola) populations from CRRI farm, Amana and Kamakhyanagar in Odisha and from Trichy in Tamil Nadu. Each rice cultivars showed differential reaction pattern to nematode populations, indicating the existence of variation in virulence pattern of root-knot nematode populations. Genomic polymorphisms between four rice root-knot populations were assessed by using 17 random primers. A total of 142 bands were amplified, out of which 95(66.9%) were polymorphic. The number of bands per primer ranged from two to fourteen with an average of 8.35 bands per primer. Forty four unique bands were identified, which could be developed into diagnostic markers to identify rice root-knot nematode population. UPGMA cluster analysis classified four populations into two major groups at 48% of genetic similarity. All the Odisha populations were included in first major cluster while Trichy population was included in second major cluster. The host reaction and molecular genotyping of four populations of the rice root-knot nematode indicates the existence of pathotype variability.