Four Sarcocystis species, i.e., Sarcocystis fusiformis and Sarcocystis buffalonis with cats as definitive hosts, Sarcocystis levinei with dogs as definitive host, and Sarcocystis dubeyi with unknown definitive host, have previously been described from water buffalo (Bubalus bubalis). The aim of the present study was genetic characterization of the causative agent(s) of water buffalo sarcocystosis in Khuzestan Province, western Iran. RFLP-PCR and partial sequence analysis of 18S rDNA gene were used for the genetic characterization of the specimens directly obtained from water buffalo. In RFLP-PCR, four restriction enzymes (Dra1, Ssp1, Fok1 and Bsl1) were used for species discrimination of Sarcocystis spp. in this host. Comparison of the molecular sequencing results and RFLP-PCR pattern of the samples obtained in the present study with those previously reported for different Sarcocystis spp. revealed that all positive Sarcocystis samples represented S. fusiformis. To our knowledge, this is the first demonstration of the existence of S. fusiformis in the Iranian water buffalo population by a genetic approach. In addition, comparison between the alignments between the Iranian 18S rDNA sequences (HQ703791), made in this study, and those previously reported for S. fusiformis in different geographical location (accession nos. AF176927, AF176926, and U03071) showed the occurrence of local genetic polymorphisms and heterogeneity in this ribosomal locus. Despite the occurrence of some genetic variations in the hypervariable regions of the 18S rDNA in S. fusiformis, Dra I restriction site was conserved among all sequences available. According to the present study, it seems that cats have a more significant epidemiological role than dogs in transmission of sarcocystosis agent to water buffalo in Iran.