Abstract: Understanding the genetic diversity at molecular level is a prerequisite in developing strategies for effective conservation and utilization of chicken genetic resources. We studied the genetic variation within and between Bangladeshi native (Naked Neck, Frizzle and Non-descriptive indigenous) and exotic (White Leghorn, Rhode Island Red, Commercial layer and broiler) chicken populations by Random Amplified Polymorphic DNA (RAPD). Four out of the 20 random primers exhibited sufficient variability for studied populations. The four primers yielded a total of 39 distinct bands, 25 of which were polymorphic. Estimation of polymorphic loci, intra-population similarity indices and Nei’s gene diversity suggested that genetic diversities within a population were high in non-descriptive, Frizzle, Naked Neck, Rhode Island Red and White Leghorn chicken populations compared to the commercial layer and broiler populations. The coefficient of gene differentiation (GST = 0.34) and gene flow (Nm = 0.98) values reflected a high level of population differences. UPGMA dendrogram segregated the chicken populations in various degree based on their genetic distance. The overall genetic distance among native chicken was relatively low comparison to the exotic populations. The results of present study might have significant impact on the breeding and conservation of native chicken genetic resources in Bangladesh.