Schistosomiasis remains a significant public health concern in many parts of sub-Saharan Africa, including Nigeria. It is caused by parasitic flatworms of the genus Schistosoma, with Schistosoma haematobium and Schistosoma mansoni being the most common species affecting the urogenital and intestinal tracts respectively. This study was aimed at investigating the prevalence of urogenital and intestinal schistosomiasis among school children of Owena community in Ondo, Ondo State, Nigeria. A cross-sectional descriptive study was conducted using convenience sampling method to compare the prevalence of urogenital and intestinal schistosomiasis among young individuals in Owena, Ondo East Local Government Area, Ondo State, Nigeria. A total of 100 participants were sampled, out of which all provided urine samples, and 51 provided stool samples. The urine samples were examined for Schistosoma haematobium by centrifugation, while the stool samples were processed using the formol-ether concentration technique to detect Schistosoma mansoni eggs. Two of the 100 urine samples tested positive for S. haematobium, representing 2.0 % prevalence, and one out of 51 stool samples tested positive for S. mansoni, indicating 1.96 % prevalence. Notably, one of the positive urine samples contained an egg with atypical morphology, lacking a terminal spine and a lateral spine, suggesting a possible hybrid schistosome egg. All positive cases recorded were among female participants. These findings indicate a low but detectable prevalence of both urogenital and intestinal schistosomiasis in the study area, with emerging appearance of parasite hybridization. The presence of hybrid eggs raises concerns about evolving parasite transmission dynamics and highlights the need for further study and molecular investigation in the area.