| Summary: | Schistosomiasis remains a public health concern in Zambia. Urinary schistosomiasis caused by <i>Schistosoma haematobium</i> is the most widely distributed infection. The aim of the current study was to determine the prevalence and risk factors of urinary schistosomiasis and identify the strain of <i>S. haematobium</i> among children in the Siavonga and Lusaka districts in Zambia. Urine samples were collected from 421 primary school children and <i>S. haematobium</i> eggs were examined under light microscopy. A semi-structured questionnaire was used to obtain information on the socio-demographic characteristics and the potential risk factors for urinary schistosomiasis. DNA of the parasite eggs was extracted from urine samples and the internal transcribed spacer gene was amplified, sequenced and phylogenetically analysed. The overall prevalence of <i>S. haematobium</i> was 9.7% (41/421) (95% CI: 7.16–13.08), male participants made up 6.2% (26/232) (95% CI: 4.15–9.03), having a higher burden of disease than female participants who made up 3.5% (15/421) (95% CI: 2.01–5.94). The age group of 11–15 years had the highest overall prevalence of 8.3% (35/421) (5.94–11.48). Participants that did not go fishing were 0.008 times less likely to be positive for schistosomiasis while participants whose urine was blood-tinged or cloudy on physical examination and those that lived close to water bodies were 9.98 and 11.66 times more likely to test positive for schistosomiasis, respectively. A phylogenetic tree analysis indicated that <i>S. haematobium</i> isolates were closely related to pure <i>S. haematobium</i> from Zimbabwe and hybrids of <i>S. haematobium</i> × <i>S. bovis</i> from Benin, Senegal and Malawi. The current study shows that urinary schistosomiasis is endemic in the study areas and is associated with water contact, and <i>S. haematobium</i> isolated is closely related to hybrids of <i>S. bovis</i> × <i>S. haematobium</i> strain, indicating the zoonotic potential of this parasite.
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