For the first time, Boliwong, an indigenous community in the Philippines was surveyed for the prevalence of Cryptosporidium within the periods of April to December 2017 . Cryptosporidium oocysts were detected from the river, creek, and water pumps via immunomagnetic separation techniques. Detections were also done from human and animal concentrated fecal samples using Modified Ziehl Neelsen technique. From the 24 water samples, seven (29.16%) were positive for Cryptosporidium with the highest concentration (0.8 oocysts/L) detected in creek. Of 35 fecal samples coming from different animal groups, eight (21.62%) were positive for Cryptosporidium oocyst. The highest intensity of oocysts shedding was detected in dogs (95% CI=5.255, 11.745). From the 137 human fecal samples, 39 (28.5%) were infected with Cryptosporidium. In this study, three risk factors were associated to the infection including (a) location (cOR= 16.39; 95% CI= 2.11-127.41; p<0.008), (b) drinking water from the natural spring (cOR=0.29; 95% CI=0.11-0.82; p<0.020), and (c) using an open pit as sanitary toilet facility (cOR=2.44; 95% CI=1.14-5.20; p<0.021). When the cOR was adjusted, using an open pit as sanitary toilet facility remained a significant risk factor of infection (aOR=0.414; 95% CI= 0.19-0.90; p<0.02). There is a potentially emerging Cryptosporidium zoonosis in Boliwong, Lagawe, Philippines. It is recommended to rehabilitate the toilet facilities and the water system in the community to avoid any possible disease outbreak. Health education is also needed in the community to maintain proper hygiene and sanitation practices.