Echinococcus granulosus sensu lato (s.l.) is a tapeworm, which causes cystic echinococcosis (CE). It dwells in small intestines of definitive hosts, where it produces eggs, which are excreted into the environment. Intermediate hosts, such as sheep, cattle, pigs, goats, horses and humans become infected with ingestion of food, contaminated with eggs. After the infection, the larval stage results in the formation of echinococcal cysts, which are located mainly in liver. For better understanding of tapeworm transmission and epidemiological features, genotype of tapeworm is determined with genotyping methods. In this study we used 15 samples of echinococcal cysts obtained from patients with CE, and 5 samples obtained from pigs with CE. Genotyping was performed with amplifying and sequencing of mitochondiral (cox1, nad1, nad5, rrnS and rrnL) and nuclear genes (18S rRNA). Genotype was successfully determined in 10/15 of samples, obtained from patients (66,7 %) and 5/5 samples, obtained from pigs. From successfully genotyped samples from patients we determined E. granulosus genotype G1 in 5/10 (50 %) samples, E. granulosus genotype G3 in 1/10 (10 %) samples and E. canadensis genotype G7 in 4/10 (40 %) samples. In all echinococcal cysts samples, obtained from pigs, we determined E. canadensis genotype G7, which is distinctive causative agent for CE in pigs.