Cystic echincoccosis (CE) is a major medical and veterinary concern in the world, especially in Iran. Domestic intermediate hosts are an important reservoir for the disease spread. The purpose of this study was to determine the prevalence of CE in slaughtered livestock in Jahrom, south of Iran. In this cross-sectional study, a total of 3074 animals (2325 (75.63%) goats, 423 (13.76%) sheep, and 326 (10.60%) cattle) were inspected macroscopically for CE. In this regard, a questionnaire about the age, sex, infected organ, number of cysts, and cyst fertility was accomplished for each animal. Moreover, PCR was applied by using the cytochrome c oxidase I (COX1) and NADH dehydrogenase subunit 1 (nad1) fragments of parasite mitochondrial genomes on some positive samples. Prevalence of CE in sheep, cattle, and goats was 11.34% (48/423), 11.04% (36/326), and 2.79% (65/2325), respectively. In all livestock, CE was more common in females than males. Moreover, the highest infection rate was observed in the age group of more than 72 months. Considering the fertility of cysts, the ratio of the number of fertile cysts to total cysts in sheep and goats were 83.3% (40/48) and 80% (52/65), respectively. All hydatid cysts were infertile in cattle. With regard to the location of the cyst on internal organs, the most were observed in the lungs and liver. Regarding the intensity of infection, 1–5, 6–9 and ≥ 10 cysts were detected in 78.52% (117/149), 6.71% (10/149) and 10.73% (16/149) of infected livestock, respectively. In all livestock, hydatid cyst with a diameter of 1–5 cm was the most frequent with 71.81% (107/149). All 149 cyst samples were subjected to PCR. Among them, a total of 18 samples (six samples of each animal) were prepared for sequencing. G6 was the most dominant. According to the results of present study and the relatively high prevalence of CE in slaughtered livestock in Jahrom, health policy makers, health authorities, and experts should make effective approach in this regard, and implement careful inspections.