Background There are growing concerns that communities characterized with surface water, where both humans and livestock interact for agricultural, domestic, cultural, and recreational purposes, are likely to support hybridization between schistosome species infecting humans and livestock. This study therefore investigated the possible human infections with hybrid schistosomes in four schistosomiasis endemic communities along the banks of Oyan dam in Ogun State, Nigeria. Methods Human urine samples were collected in Imala-Odo, Abule-Titun, Apojula and Ibaro-Oyan communities. Recovered eggs were counted, photographed, and measured with IC Measure™ for Total Length, Maximum Width, and a ratio of egg shape. Eighty-seven unusual Schistosoma eggs shaped were molecularly characterised by PCR amplification of Schistosoma specific Dra1 gene. The amplicons were further subjected to PCR amplification of schistosome ITS-2 rDNA and right representative samples with varying gel band sizes were sequenced. Results A total of 1,984 Schistosoma eggs were analysed. The egg morphometrics were within the range of 70.90 - 262.30 µm and 30.10 - 102.60 µm for total length and width respectively. The length to width ratio was 1.60 - 4.06µm. Majority of the eggs have the typical round-to-oval shaped eggs (1345, 67.8 %), followed by eggs with atypical spindle-shaped (639, 32.2 %) and eggs without spines (22, 1.1 %). Egg morphotypes were significantly different (p = 0.017). PCR amplification of Dra1 gene and ITS2 confirmed 54 (62.1%) of the eggs and 33 (61.1%) of Schistosoma origin. Sequencing of two of the DNA samples produced sequences similar to vertebrate S. magrebowiei (accession number UZAI01000474.1) and Asian S. japonicum (accession number SKCS01001458.1). Conclusion These findings suggest possibly that hybrids schistosome may be circulating in the human population in the study areas.