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Hydatid disease is a parasitic zoonosis caused by genotypes of the genus Echinococcus . This disease inflicts economic loses in livestock and cause public health burden in resource poor mostly in developing countries. The aim of this study was to determine the prevalence and identity of the genotypes responsible for hydatid cysts in cattle, goats and pigs slaughtered at selected abattoirs of southern provinces of Mozambique. Cysts were collected from liver and lungs and hydatid confirmation was made by cystic membrane observation and visualization of protoscoleces by light microscope. Thirty-two hydatid cysts from 817 cattle and two from 68 pigs were collected from local slaughterhouses and slabs. DNA was extracted from protoscoleces of each cyst together with the cystic membrane and amplified based on the mitochondrial subunit 1 of the cox1 and nad1 gene. The overall prevalence of hydatid cysts was 3.9% in cattle, 2.9% in pigs and none of the goats were found with cysts. All cysts collected from cattle and pigs were identified as Echinococcus ortleppi (G5) with a minimum homology of 99% on BLAST analysis. Our results confirm the presence of E. ortleppi in cattle and pigs in southern Mozambique at a low prevalence and further studies are recommended to determine the risk factors favoring the transmission of this zoonotic parasite in the resource-poor livestock farming communities of this region., Competing Interests: Conflict of interestThe authors declare that they have no competing interest., (© Indian Society for Parasitology 2021.)