Cryptosporidium spp. are common protist pathogens, and the growing popularity of pet rodents raises concerns about their potential role in zoonotic parasites transmission. However, epidemiological data on Cryptosporidium spp. in pet rodents in Yunnan Province is scarce. To examine the occurrence of Cryptosporidium spp. in pet rodents in Yunnan, we collected 762 fecal samples from four rodent species across four cities. Nested PCR and DNA sequencing were used to characterize the species and subtypes of Cryptosporidium. The occurrence of Cryptosporidium spp. in guinea pigs (Cavia porcellus), Siberian dwarf hamsters (Phodopus sungorus), Syrian hamsters (Mesocricetus auratus) and fancy rats (Rattus norvegicus domestica) was 18.7% (80/426), 17.3% (36/207), 12.5% (15/120), 0% (0/9), respectively, with an overall rate of 17.2% (131/762). According to regions, the positivity rate of Cryptosporidium spp. in Zhaotong city, Kunming city, Yuxi city and Qujing city was 21.0%, 17.9%, 16.8% and 10.5%, respectively. In terms of sampling location, the occurrence of Cryptosporidium spp. in pet markets, farms and shops was 19.5%, 18.6% and 0%, respectively. Sequence analysis of the small subunit ribosomal RNA (SSU rRNA) gene identified six Cryptosporidium species/genotypes: Cryptosporidium homai (n = 52), Cryptosporidium wrairi (n = 30), Cryptosporidium sp. hamster genotype (n = 25), Cryptosporidium andersoni (n = 20), Cryptosporidium parvum (n = 5), and Cryptosporidium muris (n = 1). Further subtyping of C. andersoni isolates using multilocus sequence typing (MLST) revealed a single subtype, with all isolates identified as A3A4A2A2. All five C. parvum isolates were identified as subtype IIdA15G1 based on the gp60 gene. Our findings demonstrated the presence of the zoonotic C. parvum IIdA15G1 subtype in pet rodents, suggesting that these animals, particularly hamsters, may serve as reservoirs for human-pathogenic Cryptosporidium species. These results underscore the need for improved biosecurity and husbandry practices in the pet rodent trade to mitigate public health risks.