BACKGROUND: Cystic echinococcosis (CE) or hydatid disease is a neglected, economically important zoonotic disease endemic in pastoralist communities, in particular the Turkana community of Kenya. It is caused by the larval stage of the highly diverse species complex of Echinococcusgranulosus sensu lato (s.l). The situation on the genetic diversity in humans in Kenya is not well established. OBJECTIVE: To characterise Echinococcus granulosus (s.1) species/strains isolated from humans undergoing surgery in Turkana, Kenya. DESIGN: A Cross sectional study. SETTING: The Kakuma Mission Hospital and Centre for Microbiology Research, Kenya Medical Research Institute. SUBJECTS: Eighty (80) parasite samples from 26 subjects were analysed by Polymerase chain reaction--Restriction fragment length polymorphism (PCR-RFLP) targeting the nad 1 gene for molecular characterization. RESULTS: Two different genotypes of E. granulosus were identified from the samples analysed: E. granulosus sensu stricto (G1-G3) 85% of the samples analysed and E. canadensis G6/7 (15%). Most of the hydatid cysts (35%) were isolated from the liver. Other sites where cysts were isolated from include: kidney, abdomen, omentum, retroperitonium and the submandibular. Majority of cysts presented as CE1 (50%) and CE3B (42%) images according to WHO ultrasound classification. Both males and females were infected with E. granulosus s.s but only the females showed infection with E. canadensis G6/7. Chi-square test revealed significant difference between age of individuals and cysts classification by ultrasound. In addition, there was an association between cyst presentation (single or multiple) and genotype whereby all the E. canadensis G6/7 cases presented as single cysts in the infected persons. CONCLUSION: This study corroborates previous reports that E. canadensis G6/7 strain is present in Turkana, a place where initially only E. granulosus s.s (G1-G3) was known to be present and that E. granulosis (G1-G3) remains the most widespread genotype infecting humans in the Turkana community.