The genetic variability of the lymphatic filarial parasite Wuchereria bancrofti, from three localities (one urban and two rural areas) in southern India, endemic for filariasis was studied using random amplified polymorphic DNA (RAPD) markers. The RAPD profiles were generated for 21 parasite populations (7 populations from each area), using a 10-mer random primer. The analysis of profiles indicated the existence of considerable genetic variability among parasite populations. The Nei's gene diversity between the individual populations in the 2 areas (one urban and another rural) was comparatively greater (0.3372+/-0.1462 & 0.2830+/-0.1764) than that of populations in another village (0.0490+/-0.1373). The greater genetic diversity among the former areas may be due to human migration, endemicity for long time and drug (diethyl-carbamazine citrate) pressure unlike the populations of latter village where the filariasis is relatively a recent introduction and which was never under active chemotherapy. The Nei's genetic distance was estimated and the phylogenetic tree was constructed using 'UPGMA'. These analyses indicated the prevalence of at least two genetically distinct clusters, among the populations studied, their maximum genetic distance being 0.2444. The finding of two genetic 'variants' of W. bancrofti, in the present study, may have important implications in filariasis epidemiology and control/elimination programmes.