<p>Cystic echinococcosis is an important zoonotic disease and pose a significant health threat worldwide. <i>Echinococcus granulosus</i> (<i>E. granulosus</i>) has ten strains and exhibits many characteristics. Hence, the current study aims to identify the hydatid cysts genotype isolated from sheep and goats in Rasht County through morphological and molecular analyses. During 6 months (winter 2018 to summer 2019), 50 samples, including liver and lung tissues, were collected at Rasht County slaughterhouse (30 goats and 20 sheep). Hydatid cyst fluid (HCF) was extracted, and protocoleces were collected and rostellar hooks’ morphological parameters were examined. DNA was extracted, polymerase chain reaction (PCR) was performed using primers on the ITS 1 gene using EgF and EgR, and the enzyme Bsh1236 I was used for digestion. The morphological and molecular analysis identified sheep and goat hydatid cyst isolated as strain G1-G3. This study highlights the importance of carefully monitoring the prevalence of hydatid disease in Rasht, Iran, especially in small ruminants. It is especially important for future studies in strain identification and awareness-raising about methods for preventing and controlling zoonotic diseases caused by <i>E. granulosus</i>. This research can be considered important for epidemiological studies and examining how the parasite spreads in other regions of the country and even globally in the face of drug resistance and common diseases between humans and livestock.</p>