Species of Cryptosporidium are ubiquitous parasites capable of infecting numerous animal species and humans. Wild rodents are naturally infected by Cryptosporidium via contaminated environment. In order to examine the prevalence of Cryptosporidium in wild rodents in Thailand and understand the potential role played by rodents in transmission, 117 fecal samples obtained from trapped rodents from Nan, Songkhla, and Tak provinces of Thailand were examined using 18S RNA gene for a PCR screening test. The overall prevalence of Cryptosporidium spp. was 23.1 % (27/117) and, after sequencing, classified as Cryptosporidium meleagridis C. parvum, C. suis, C. viatorum and C. wrairi. Seven rodent species from a total of 15 species showed infection: Rattus tanezumi, R. exulans, R. andamanensis, Berylmys bowersi, Bandicota indica, Maxomys surifer, and Niviventer fulvescens with Niviventer fulvescens (1/1 specimen infected). Rodents from Nan province was highly infected (34.8%, 8/23) compared to those from Tak (20.6%, 7/34) and Songkhla (20%, 12/60). Cryptosporidium spp prevalence varied according to habitat types where rodents were trapped: rice field (33.3%, 5/15), plantation/orchad (29.6%, 8/27), forest (25%, 9/36) and house (14.7%, 5/34). Cryptosporidium genotypes' diversity was found correlated with the diversity of rodents. These results suggest that small mammals, and particularly rodents, might play a potential role as carriers and reservoirs for Cryptosporidium transmission among animals as well as to humans.