BackgroundBlastocystis spp. is one of the most common protozoa worldwide, living in the gastrointestinal tract of humans and many other animals. On the basis of the genetic heterogeneity of small subunit ribosomal RNA, at least 28 subtypes (ST1‐ST17, ST21 and ST23–ST32) are reported to exist in mammals and birds.ObjectivesThis study was carried out to determine the prevalence and subtypes of Blastocystis spp. in Anatolian buffaloes (Bubalus bubalis) in Van province in the Eastern Anatolia Region of Turkey.MethodsDNA was extracted using commercial GeneMATRIX Stool DNA Purification Kit and then stored at −20°C until PCR amplification. After PCR amplification of the SSU rRNA gene region positive Blastocystis spp., amplicons from buffalo faeces were sequenced and then deposited in GenBank (OR576949.1, OR576950.1, OR576970.1, OR576971.1, OR577019.1, PP837943.1, PP837940.1, PP837939.1, PP837604.1, PP837937.1, PP837934.1, PP837601.1, PP837936.1 and PP837603.1).ResultsPCR analysis of 120 faecal samples showed a total prevalence of 11.67% (14/120). The prevalence was higher in females and young animals (p > 0.05). Sequence analysis revealed Blastocystis spp., ST10, ST14, ST25 and ST26 subtypes. To our knowledge, Blastocystis subtypes ST25 and ST26 in buffaloes were reported for the first time in this study.ConclusionIt is thought that more large‐scale studies should be carried out to determine the zoonotic subtype potential of this protozoan in the region.