The study was conducted to determine the role of house flies, Musca domestica and Musca sorbens to carry Cryptosporidium species in natural environment and filth flies potential for contamination of food item they visited using acid-fast stain technique. Cryptosporidium was identified from flies collected in dairy cow barns, butchery, market and defecating grounds. Musca domestica captured from dairy cow barns and M. sorbens from defecating ground were found carrying more oocyst of Cryptosporidium parvum. Oocyst load per fly for M. domestica and M. sorbens was 5.84 and 3.42, respectively. Flies’ population dynamics in each month had little relation to the monthly oocyst frequency, r = 0.06 and 0.02 for M. domestica and M. sorbens, respectively. Cryptosporidium species oocysts were isolated from frozen mango juice, which filth flies visited in dairy farm barn. Load of oocysts in the mango juice was dependent on time contact of flies with mango juice and more oocysts were recovered (P < 0.05) in mango juice samples accessed by filth flies for longer period. Role of filth flies to carry and deposit Cryptosporidium species oocyst for development of food-borne cryptosporidiosis is signified.