BackgroundIndia contributes 1.5–2 million annual confirmed cases of malaria. Since both parasites and vectors are evolving rapidly, updated information on parasite prevalence in mosquitoes is important for vector management and disease control. Possible new vector-parasite interactions in Goa, India were tested.MethodsA total of 1036 CDC traps were placed at four malaria endemic foci in Goa, India from May 2013 to April 2015. These captured 23,782 mosquitoes, of which there were 1375 female anopheline specimens with ten species identified using morphological keys. Mosquito DNA was analysed for human and bovine blood as well as for Plasmodium falciparum and Plasmodium vivax infection.ResultsHuman host feeding was confirmed in Anopheles stephensi (30 %), Anopheles subpictus (27 %), Anopheles jamesii (22 %), Anopheles annularis (26 %), and Anopheles nigerrimus (16 %). In contrast, Anopheles vagus, Anopheles barbirostris, Anopheles tessellates, Anopheles umbrosus and Anopheles karwari specimens were negative for human blood. Importantly, An. subpictus, which was considered a non-vector in Goa and Western India, was found to be a dominant vector in terms of both total number of mosquitoes collected as well as Plasmodium carriage. Plasmodium infections were detected in 14 An. subpictus (2.8 %), while the traditional vector, An. stephensi, showed seven total infections, two of which were in the salivary glands. Of the 14 An. subpictus infections, nested PCR demonstrated three Plasmodium infections in the salivary glands: one P. vivax and two mixed infections of P. falciparum and P. vivax. In addition, ten gut infections (one P. vivax, six P. falciparum and three mixed infections) were seen in An. subpictus. Longitudinal mosquito collections pointed to a bimodal annual appearance of An. subpictus to maintain a perennial malaria transmission cycle of both P. vivax and P. falciparum in Goa.