Levels of genetic diversity vary dramatically between Blastocystis subtypes

► We examined the intrasubtype diversity in Blastocystis ST3 and ST4 from primates. ► ST3 shows vast genetic variation as opposed to the almost clonal ST4. ► Homogeneity of ST4 indicates relatively recent colonisation of humans. ► Anthroponotic transmission appears most common despite some evidence of zoonotic transmission. ► MLST is a powerful tool for molecular epidemiological studies of Blastocystis.