A total of 123 fecal samples of slaughtered finisher pigs and 21 sows from 14 farms were screened for Cryptosporidium spp. infection using the aniline-carbol-methyl violet staining method. Positive samples were molecularly characterized by direct sequencing of partial small subunit ribosomal RNA (SSU rRNA) and GP60 partial genes and polymerase chain reaction restriction fragment length polymorphism of SSU rRNA. Cryptosporidium oocysts were microscopically identified in 36 finishers (29%) and two sows (10%). Twenty-one mono-infections of Cryptosporidium pig genotype II and 15 mixed-infection of Cryptosporidium pig genotype II and Cryptosporidium suis in finishers were found. Both sows were infected with the Cryptosporidium parvum subgenotype IIaA16G1R1, which is reported from pigs for the first time.