Investigations into the genetic strains of Echinococcus granulosus parasites occurring in sheep and cattle in Turkey were undertaken. A total of 112 hydatid cysts were investigated from sheep (100 isolates) derived from widely distributed sites within Turkey as well as from cattle (12 isolates) from the Turkish province of Kars. The parasite genotypes in these isolates were determined by DNA sequencing of part of the mitochondrial Cytochrome C oxidase 1 (cox1) gene. Haplotypes were identified which corresponded clearly to the previously described strain G1 in a total of 107 isolates, including 98 isolates from sheep and 9 isolates from cattle. Five isolates, including 2 sheep and 3 cattle, were determined to belong to the G3 genotype. Parasites of the G3 genotype were identified only in isolates derived from animals in the eastern regions of Turkey. While the majority of the isolates described here had haplotypes corresponding to the G1 genotype, none matched exactly the G1 sequence that was defined in previous studies. Analysis of all GenBank entries for E. granulosus cox1 sequences representing G1, G2 and G3 genotypes identified substantial microsequence variability. G1 and G3 could be distinguished as separate strains, however, the existence of G2 as a separate strain could not be supported. Rather, this can be regarded as a microsequence variation of G3.