Cryptosporidium spp. are common protozoan parasites that can infect humans and animals worldwide. Recently, the hairless guinea pigs (also called Skinny pigs) were introduced into China as pets. However, Cryptosporidium species and their prevalence in these exotic animals were not studied. In this study, fecal samples were collected from a total of 324 hairless guinea pigs from a pet market and four breeding facilities in four provinces of China. The infection rate of Cryptosporidium was 6.8% (22/324). Three Cryptosporidium species were identified, including Cryptosporidium homai (n = 16), Cryptosporidium wrairi (n = 5), and Cryptosporidium hominis plus C. homai (n = 1). Sequence analysis of the small subunit (SSU) rRNA gene showed that the C. hominis isolate was a C. hominis variant, which mostly infects equine animals. However, the identification of C. hominis was not supported by the analysis of other genetic loci. The C. hominis isolate was characterized as C. homai at both 70-kDa heat shock protein (hsp70) and actin genes, indicating a mixed infection. At the 60-kDa glycoprotein (gp60) gene, subtyping of the C. hominis isolate was not successful. Five C. wrairi isolates were identified as subtype VIIaA13T1, which was previously reported in a guinea pig in the USA. The Cryptosporidium spp. identified in this study have no or low zoonotic potential.