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Cryptosporidium is one of the most important causes of diarrhoea in children less than 2 years of age, but little is known about the molecular characterization of Cryptosporidium species in Mozambique. This study aimed to determine the frequency, associated factors and determination of Cryptosporidium species and genotypes in children admitted to two public hospitals in Maputo, Mozambique under the National Surveillance of Acute Diarrhoea. We studied 319 patients 0-60 months old, admitted for acute diarrhoea between April 2015 and February 2016. Clinical and epidemiological characteristics were accessed using a structured questionnaire and stool samples were examined for the presence of Cryptosporidium spp. oocysts using Modified Ziehl-Neelsen staining technique. DNA was isolated from 192 samples and analyzed using Polymerase Chain Reaction (PCR) and Restriction Fragment Length Polymorphism (RFLP) based on the Cryptosporidium 18S ribosomal RNA gene. Statistical analysis was performed in SPSS v. 19.0 (IBM Company ©, USA). Overall, 57.7% (184/319) were males and the median of age (InterQuartil Range, IQR) was 11.0 (7-15) months. Cryptosporidium spp. oocysts were detected in 10.97% (35/319) by direct microscopy. The caregiver’s age range and the lack of formal education and the child diet based on artificial milk constituted significant risk factors for acquiring the infection. Cryptosporidium spp. DNA was recovered from 35.4% (68/192) by conventional PCR and C. hominis infection (93.1%, 27/29) was the most common, followed by C. parvum bovine genotype (3.4% 1/29) and a mixed infection with C. hominis and C. parvum bovine genotype (3.4%, 1/29). These results suggest that C. hominis is the major cause of cryptosporidiosis in Maputo and show important implications for public health because it reveals that health education actions and improvements in sanitary and nutritional conditions can significantly reduce cryptosporidiosis in Maputo. Keywords: C. hominis, C. parvum, Children, Acute diarrhoea, Maputo