Blastocystis sp. is a single-cell microorganism occurring in the gastrointestinal tract of humans and various animals and is distributed worldwide. Blastocystis exhibits extensive genetic diversity of 28 subtypes (STs) based on the small subunit ribosomal RNA (SSU rRNA) gene. In this study, the genetic diversity and zoonotic potential of Blastocystis were evaluated using pig faecal samples from two farms in Slovakia. Blastocystis spp. were detected in pigs intended for distribution and consumption. ST 5 subtype was identified in all positive samples and age categories with a prevalence of 12%. However, the prevalence on one of the farms was up to 28.6%. This is the first study of Blastocystis in pigs carried out in Slovakia. Although a number of samples obtained was small, the identified subtype of ST5 Blastocystis sp. occurs in humans and animals. It may have zoonotic potential and therefore may be a risk factor due to the close contact between humans and pigs on the breeding farms.