The diversity and importance of Echinococcus species in domesticated animals in Kazakhstan are poorly understood. In this study, 17 cysts of Echinococcus were collected from cattle and a further 17 cysts from sheep. DNA was extracted from the individual cysts and used for polymerase chain reaction amplification of mitochondrial subunit 1 of the cox1 and nadh1 gene. Amplicon sequencing results revealed the presence of Echinococcus granulosus sensu stricto G1 in 15 cattle and 15 sheep, and G3 genotype from two cattle. Echinococcus canadensis (G6/G7 strain) was found in two cysts originating from sheep.