A very high prevalence of microfilaremia of 42.68 per cent out of 164 canine blood samples examined was observed in Cherthala (of Alappuzha district of Kerala state), a known humanBrugia malayiendemic area of south India. The species of canine microfilariae were identified asDirofilaria repens, Brugia malayi, andAcanthocheilonema reconditum.D. repenswas the most commonly detected species followed byB. pahangi.D. immitiswas not detected in any of the samples examined. Based on molecular techniques, microfilariae with histochemical staining pattern of “local staining at anal pore and diffuse staining at central body” was identified asD. repensin addition to those showing acid phosphatase activity only at the anal pore. Even thoughB. malayilike acid phosphatase activity was observed in few dogs examined, they were identified as genetically closer toB. pahangi. Hence, the possibility of dogs acting as reservoirs of humanB. malayiin this area was ruled out.