Sixty-six isolates of larval stage of Echinococcus granulosus, a known pathogenic parasite of man and animals were collected from cattle, buffalo, sheep, and goats. Single-stranded conformation polymorphism (SSCP) for analysis of variation after denaturation of amplicon of intron of actin II (ACTII) revealed six SSCP phenotypes. Intron portion was analyzed considering introns-early and introns-late theories. Isolates belonging to different conformers were further screened for mitochondrial ATPase subunit 6 (ATP6) and NADH dehydrogenase subunit II (nadII) genotypes. Assignment of each isolate to its specific strain was achieved after comparing with standard genotypes of E. granulosus. Variants deduced by nuclear targets did not match with mitochondrial haplotypes. A possible explanation for this observation can be attributed toward interspecific hybridization since cross-fertilization occurs less frequently in hermaphrodite organisms. A phylogenetic tree drawn on the basis of predicted aminoacid sequence of ATP6 and nadII revealed two distinct clusters i.e. E. granulosus sensu stricto and E. ortleppi/cattle strain (EG5). To the best of our knowledge, this is the first report of genetic characterization of two distinct ATP6 and nadII genotypes of zoonotic importance living in sympatry.