The genus pseudomonas spp., are able to metabolise the petrochemical pollutants in the environment, and as a result can be used for bioremediation. Naphthalene is a major component in the petroleum that can cause damages the surrounding ecosystems. The pollutant may inhibit some microbial communities that are important in some biogeochemical cycles of that ecosystem and this affects the productivity of such ecosystems. The aim of present study was to investigate the genetic diversity of naphthalene degrading Pseudomonas aeruginosa by using random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) method. The petroleum contaminated three different kinds of soil sample like A. petrol, B. diesel, and C. both (A&B) were collected from petrol spilling, diesel spilling and petrol+diesel spilling sites respectively in Tamil Nadu. The pure culture of P.aeruginosa isolated from cetrimide agar and this species conformed through gram staining, and various biochemical analyses. The naphthalene degrading P.aeruginosa conformed by catechol as metabolic intermediates in the substrate of naphthalene. The species of interest genetic diversity was done by RAPD-PCR method and gel image creates dendogram analysis. RAPD-PCR was carried out to determine the genetic diversity of P.aeruginosa in the petroleum by-products contaminate soil samples. Totally 39 bands was amplified by using five random (OPW-6 to 10) short singe primers. In the present study, we found that RAPD-PCR technique as a useful tool for investigation of the genetic diversity among P.aeruginosa and the number of bands and banding pattern were variable depending upon the primer and the type of species tested. This also study showed that a relative high polymorphism among P.aeruginosa isolates from sample A and C than B.