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Echinococcus granulosus sensu lato causes Cystic echinococcosis. This study investigated the bacterial and fungal species in the liver and lung hydatid cysts obtained from sheep, goats, cattle, and camels slaughtered in Yazd abattoir, Central Iran. In this study, 84 hydatid cysts were obtained from 20 sheep, 13 goats, 25 cattle, and 26 camels. The fertility and viability rates were assessed using light microscopy and eosin staining, respectively. The aspirated hydatid cysts were cultured to detect the presence of any bacteria and fungi. Bacterial isolates were identified by biochemical tests. DNA was also extracted from germinal layers, and then genotyping was carried out targeting the cox 1 gene. The statistical analysis was performed by SPSS version 16.0. This study showed that 22.62% (19/84) of hydatid cysts had bacterial occurrence, and none of the samples had fungal species. Among the fertile cysts, 52.6% had bacterial occurrence, of which 40% were viable. Most bacteria detected in hydatid cysts included Staphylococcus saprophyticus, Escherichia coli, and S. epidermidis. Hydatid cysts with bacterial occurrence were identified as G1-G3, G5, and G6/G7. The bacterial species occurrence in hydatid cysts had no significant relationship with fertility and viability (P > 0.05), without any significant relation with viability (P > 0.05), animal species (P > 0.05), involved organ in animals (P > 0.05), and hydatid cyst genotypes (P > 0.05). It should also be mentioned that this is the first study to assess the relationship between hydatid cyst genotyping and the occurrence of fungal and bacterial species., (© 2022. The Author(s), under exclusive licence to Springer Nature B.V.)