The purpose of this study was to genotypically characterize and phylogenetically analyze the 18S rDNA sequences of Cryptosporidium obtained from poultry in Brazil. Fecal samples were obtained from ducks, chicks and quails sold in popular markets. DNA was isolated from Cryptosporidium positive feces, and 18S subunit rDNA was amplified and processed using nested-polymerase chain reaction (PCR). To identify the protozoan species, the PCR amplicons were used for restriction fragment length polymorphism (RFLP) and sequencing analyses. The presence of Cryptosporidium oocysts was observed in 76% of the ducks, 55% of the quails and 86% of the chicks. Sequencing and further phylogenetic analyses identified C. parvum in quails and chicks and C. baileyi in ducks. Although C. baileyi is usually a parasitic species found in birds, C. parvum, due to its weak host specificity, is the species most frequently diagnosed in various domestic and wild animal species, especially mammals. Thus, suggesting that the poultry observed in the present study would be considered as mechanical transporters of C. parvum, contributing to protozoa environmental dissemination.