Extensive genomic polymorphism has been demonstrated among morphologically identical Blastocystis isolates. To this end, 32 Blastocystis isolates from the Philippines (12 from humans, 12 from pigs and 8 from chickens) were analyzed genetically by riboprinting or restriction fragment length polymorphism (RFLP) analysis of polymerase chain reaction (PCR) amplified small subunit rDNA. Three distinct riboprint patterns were observed from the HinfI digestion, while four patterns resulted from the RsaI digestion of Blastocystis SSU rDNA. Restriction fragment profiles between Blastocystis isolates from different hosts were generally different from each other. However, Blastocystis isolates within each host group were practically the same. Cluster analysis of the riboprint patterns revealed seven distinct groups of the Blastocystis isolates, including a zoonotic strain. These results demonstrate the genetic heterogeneity of Blastocystis in the Philippines and a support to the idea of the organism's zoonotic potential.