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Introduction: Cryptosporidium is an important cause of diarrhea in children and immune-compromised individuals. Recent advances in molecular diagnostics have led to the discovery of subtype families that are thought to be more commonly associated with diarrhea. We aimed to isolate and characterize Cryptosporidium spp among children with diarrhea in Jos, Nigeria., Methods: Stool samples were collected from165 children aged 0-5 years with diarrhea. Cryptosporidium oocysts were examined by wet mount preparation, using formalin ether and a modified acid fast staining method. DNA was extracted from positive samples using QIAamp DNA stool mini kit and PCR-RFLP assay was carried out after quantification. Genotyping and phylogenetic analysis were done to determine the subtype families and their relatedness., Results: From the 165 children studied, 8 (4.8%) were infected with Cryptosporidium. PCR-RFLP assay and genotype characterization found the following Cryptosporidium species: C. hominis 6 (75%) and C. parvum 2 (25.0%), with family subtypes Id-5, Ie-1 and IIa-1, IId-1 respectively.The most common species was C. hominis and the frequent subtype was C. hominis-Id 5 (62.5%)., Conclusion: Cryptosporidium is not an uncommon cause of diarrhea in children, with C. hominis being the dominant species. Also C. hominis Id is the commonest sub-family subtype. Put together, zoonotic species may be an important cause of diarrhea in children aged 0-5 years in Jos, Nigeria., Competing Interests: The authors declare no competing interests.