Cryptosporidium spp. were detected in 17 of 135 swine lagoon samples from five farms by 18S ribosomal DNA locus and PCR. Seventeen positive samples identified were included two distinctive genotypes C. suis and Cryptosporidium sp. based on a small-subunit rRNA gene-based PCR-restriction fragment length polymorphism analysis. Cryptosporidium spp. were detected out of farrowing, farrowing and nursery (mix), and finishing. Prevalence rate was 12.6% with infection rates between 3.7 and 18.5%. We concluded that Cryptosporidium oocysts can persist in treated lagoon and potentially contaminate surface water through improper discharge. This study was undertaken for the evaluation of the infection status of the genotypes of Cryptosporidium spp. in swine lagoon.