Abstract  Anopheles stephensi is the main vector of urban malaria in South Asia. Three ecological variants (‘type’, ‘mysorensis’and‘intermediate’) of An. stephensi have been reported on the basis of ecology and egg morphology. However, it is unclear if there is any genetic isolation between the three variants. We analyzed the three variants of An. stephensi using eight microsatellite loci and found that large and significant genetic differentiation exists between them (mean FST= 0.393 and mean RST= 0.422). Pairwise estimates of genetic differentiation between the variants were ‘type’ versus ‘mysorensis’ (mean FST= 0.411 and mean RST= 0.308), ‘type’ versus ‘intermediate’ (mean FST= 0.388 and mean RST= 0.518) and ‘intermediate’ versus ‘mysorensis’ (mean FST= 0.387 and mean RST= 0.398) and all were statistically significant (P < 0.05). The greater sensitivity of RST in differentiation indicated that mutations and not genetic drift had generated the differences between three variants of An. stephensi. The present study indicated large genetic differentiation and presence of non‐significant low level of gene flow between the three variants (‘type’, ‘mysorensis’and‘intermediate’) of An. stephensi.

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