Lymphatic filariasis (LF) is a leading cause of morbidity in the tropical world. It is caused by the filarial parasites Wuchereria bancrofti, Brugia malayi and Brugia timori and transmitted by vector mosquitoes. Currently a programme for the elimination of LF, Global programme for Elimination of Lymphatic Filariasis (GPELF), is underway with the strategy of mass administration of single dose of diethylcarbamazine or ivermectin, in combination with an anthelmintic drug, albendazole. However, antifilarial drugs used in the programme are only microfilaricidal but not or only partially macrofilaricidal. Hence, there is a need to identify new targets for developing antifilarial drugs. Filarial parasites harbor rickettsial endosymbionts, Wolbachia sp., which play an important role in their biology and hence are considered as potential targets for antifilarial chemotherapy development. In this study, one of the cell division proteins of Wolbachia of the major lymphatic filarial parasite, W. bancrofti, viz., filamentation temperature-sensitive protein Z (FtsZ), was explored as a drug target. The gene coding for FtsZ protein was amplified from the genomic DNA of W. bancrofti, cloned and sequenced. The derived amino acid sequence of the gene revealed that FtsZ protein is 396 amino acids long and contained the tubulin motif (GGGTGTG) involved in GTP binding and the GTP hydrolyzing motif (NLDFAD). The FtsZ gene of endosymbiont showed limited sequence homology, but exhibited functional homology with ß-tubulin of its host, W. bancrofti, as it had both the functional motifs and conserved amino acids that are critical for enzymatic activity. ß-tubulin is the target for the anti-helminthic activity of albendazole and since FtsZ shares functional homology with, ß-tubulin it may also be sensitive to albendazole. Therefore, the effect of albendazole was tested against Wolbachia occurring in mosquitoes instead of filarial parasites as the drug has lethal effect on the latter. Third instar larvae of Culex quinquefasciatus were treated with 0.25mg/ml of albendazole (test) or tetracycline (positive control) in the rearing medium for different intervals and tested for the presence of Wolbachia by FtsZ PCR. All the treated larvae were negative for the presence of the FtsZ band, whereas all the control larvae were positive. The findings of the study, thus indicated that FtsZ is sensitive to albendazole. In view of this albendazole appears to have dual targets; FtsZ in Wolbachia and ß-tubulin in W. bancrofti. Further, the functional domain of the gene was assessed for polymorphism among recombinant clones representing 120 W. bancrofti parasites, prevalent across wide geographic areas of India and found to be highly conserved among them. Since it is highly conserved and plays an important role in Wolbachia cell division it appears to be a potential target for anti-filarial chemotherapy development.