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Background Cryptosporidium is an important zoonotic parasite that is commonly found in non-human primates (NHPs). Consequently, there is the potential for transmission of this pathogen from NHPs to humans. However, molecular characterization of the isolates of Cryptosporidium from NHPs remains relatively poor. The aim of the present work was to (i) determine the prevalence; and (ii) perform a genetic characterization of the Cryptosporidium isolated from captive Macaca fascicularis and M. mulatta on Hainan Island in southern China. Methods A total of 223 fresh fecal samples were collected from captive M. fascicularis ( n = 193) and M. mulatta ( n = 30). The fecal specimens were examined for the presence of Cryptosporidium spp. by polymerase chain reaction (PCR) and sequencing of the partial small subunit ( SSU ) rRNA gene. The Cryptosporidium -positive specimens were subtyped by analyzing the 60-kDa glycoprotein ( gp60 ) gene sequence. Results Cryptosporidium spp. were detected in 5.7% (11/193) of M. fascicularis . All of the 11 Cryptosporidium isolates were identified as C. hominis . Subtyping of nine of these isolates identified four unique gp60 subtypes of C. hominis. These included IaA20R3a ( n = 1), IoA17a ( n = 1), IoA17b ( n = 1), and IiA17 ( n = 6). Notably, subtypes IaA20R3a, IoA17a, and IoA17b were novel subtypes which have not been reported previously. Conclusions To our knowledge, this is the first reported detection of Cryptosporidium in captive M. fascicularis from Hainan Island. The molecular characteristics and subtypes of the isolates here provide novel insights into the genotypic variation in C. hominis .

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