Cryptosporidiosis acutely impacts the digestive and/or respiratory tract of the birds in many species of various orders. More importantly, it is also well known as a significant zoonotic disease, which can lead to diarrhea in humans and livestock. Regarding increasing demand for free-range products and increasing the number of free-range poultry farms, the present paper evaluated histopathological and molecular detection of Cryptosporidium baileyi and Cryptosporidium parvum in free-range and commercial broiler chickens in the north part of Iran. For this purpose, 100 fecal and tissue samples of the chickens in Guilan province were collected. After microscopic examination using Ziehl-Neelsen staining, molecular analyses of the fecal samples were processed by Nested-PCR targeting the 18S rRNA gene followed by sequencing of the amplicons and phylogenetic analyses. Eventually, the tissue samples were studied for histological lesions. Findings demonstrated the presence of Cryptosporidium baileyi and Cryptosporidium parvum in 6 % and 2 % of fecal samples, respectively. This is the first identification of C.parvum in avian hosts in Iran, and for the first time, C.baileyi and C.parvum are shown in native free-range chickens in Iran. All of the PCR positive birds with clinical symptoms showed gross lesions of respiratory infections. There was no significant difference between infection rate in free-range and commercial broiler chickens; however, the infection rate was significantly higher in chickens <25 days old. To conclude, we present here a notable Cryptosporidium infection rate in the free-range chicks in Iran, which notify the role of this host as a reservoir and should be more noted due to the economic and zoonotic importance.