Hydatid cyst disease, caused by Echinococcus granulosus sensu lato (s.l.), is linked to endemic areas in the Levant region, such as Jordan. There is a scarcity of epidemiological data about this disease. Our goal was to pinpoint the particular genotypes accountable for sheep and goat infection in unexplored regions of Southern Jordan. Partial sequences of cytochrome C oxidase (Cox1, 450 bp) and NADH dehydrogenase subunit 2 (Nad2, 820 bp) of the E. granulosus from Jordan were analysed and compared with E. granulosus s.l. reference genomes, to infer the phylogeny of the species. This analysis demonstrated a significant degree of intraspecific similarity and identified the presence of E. granulosus sensu stricto (G1, G3). The G1 genotype was the most prevalent (Cox1, n = 17/17); (Nad2, n = 13/18). The study examined partial Cox1 sequences from different countries (Jordan, Lebanon, Iran, India) and regions (South America) to analyze the genetic architecture and phylogeography of the G1 genotype at regional and global levels. One primary haplotype (Hap_1) was present in the research locations. We hypothesized that a certain branch of G1, known as Hap_1, was prevalent among regions that were not geographically connected. Future research on the biology and distribution of E. granulosus s.s. will be enhanced by this information.