Anopheles barbirostris is the major vector of Timor filaria, and A. jamesii is of Bancroftian filaria in Srilanka, and is a suspected vector of malaria as it can support the sporogenic cycle of Plasmodium vivax. Deltamethrin screening revealed that A. jamesii was susceptible to deltamethrin (LC50 = 0.0025 ppm; LT50 = 11.38 min), while A. barbirostris was resistant (LC50 = 3.802 ppm; LT50 = 20.28 min). Genomic DNA isolated from the two species were used for characterisation of the insecticide resistance and susceptibility using Random Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR). 15 random primers produced 59 bands in A. barbirostris and 31 bands in A. jamesii. Out of these, 58 bands were polymorphic between the two species. The genetic distance calculated using FREE TREE software indicated 0.91549 (Nei and Li method) and 0.83824 (Jaccard method). The matrices for dissimilarity (1.358) and similarity (0.150) between the two species calculated using NTSYSpc 2.2 showed polymorphism of 88.9 %. Genetic variance between A. barbirostris and A. jamesi is probably the reason for the former to be resistant, while the latter is susceptible to deltamethrin.