Blastocystis spp. are common intestinal parasites found worldwide in humans and a wide range of animals. They exhibit extensive genetic diversity; currently, 17 subtypes (STs) and some groups called non-mammalian and avian STs (NMASTs) have been proposed. In addition, a large variety of animals have been reported as hosts of the parasite, and new hosts and STs are still being described. In this study, Blastocystis infection of wild animals in two sylvatic areas of Mexico was surveyed. Of one hundred twenty-four fecal samples, six were positive for Blastocystis: specifically, one sample from an opossum, one sample from a bat, and four samples from different species of rodents. ST4, ST17, and nucleotide sequences similar to Blastocystis lapemi were identified based on SSU rDNA sequences. To our knowledge, this is the first report to investigate species poorly or not previously evaluated for Blastocystis infection. Mammals having different niches and geographical distribution were infected with similar genetic type of Blastocystis, so that we suggest that local water or food sources could play an important role in Blastocystis transmission and ST maintenance in wild animals. Additionally, there are STs with scarce genetic variation, suggesting that they could be highly adapted to their hosts. These data contribute to our understanding of the host range and genetic diversity of Blastocystis.