Hydatidosis is an important public health problem in several parts of Iran. The aim of this molecular study is to investigate Echinococcus granulosus genotypes as the causative agents of hydatidosis in the south-west of Iran (Khuzestan province). In this study, isolates of 334 hydatid cysts were collected from the liver and lungs of 141 sheep, 104 cattle, 84 goats and 5 human cases. DNA was extracted and examined by nested polymerase chain reaction (PCR) of ribosomal DNA (rDNA) internal transcribed spacer 1 (ITS1) and restriction fragment length polymorphism (RFLP)-PCR. In addition, fragments of genes coding for ITS1 were sequenced. The results of RFLP-PCR analysis revealed the presence of the G1 genotype in all human, cattle, goat and sheep isolates. Furthermore, no camel strain (G6) was detected among all samples in the regions studied. The molecular findings indicate that the predominant genotype involved in E. granulosus transmission in south-west Iran is the common sheep strain (G1 genotype), which occurs in human, cattle, sheep and goat populations. In conclusion, these results may have important implications for hydatid disease control in the areas studied.