Random primers were used to assess the genetic variability among brown planthopper (BPH) populations from four locations of Odisha and five locations of Andhra Pradesh. A total of 137 bands were amplified by 17 random primers, of which 116 are polymorphic. Thirty four unique bands were identified, which can be useful for developing diagnostic markers. Genetic similarity between BPH populations varied from 0.346 to 0.72 with an average of 0.556, indicating that wide genetic variation exists between BPH populations at molecular level. All the populations could be uniquely distinguished from each other and grouped into two major clusters at 38% level of genetic similarity. The BPH population from Pipili, Odisha was found to be different from others. Further study with host differentials can ascertain its biotype status.