In sub-Saharan Africa’s endemic areas for urogenital schistosomiasis, male genital schistosomiasis (MGS) can cause significant morbidity. As part of the Hybridization in UroGenital Schistosomiasis investigation, an MGS sub-study examined a cohort of adult men over a calendar year to better ascertain general infection dynamics and putative zoonotic schistosome transmission. During follow-up, demographic, health and socio-economic data were collected through individual questionnaire interviews. Collected urine and semen were analysed using urine filtration, urine and semen microscopy and molecular DNA analyses of semen. Ten participants with reported MGS-associated symptoms had Schistosoma eggs in their urine and semen at 6-month follow-up, with seven at 12 months. Ten out of 11 participants with Schistosoma haematobium eggs on semen microscopy at baseline had persistent infection at 6-month follow-up, together with 6 new participants, giving an MGS prevalence of 84·2% (n = 19). Two also had Schistosoma mattheei eggs co-infection. Four of the 13 participants at 12-month follow-up had S. haematobium eggs in their semen which were persistent at all the time points. Using semen PCR, 14 participants (73·7%) had Schistosoma infection at 6 months, with only 2 participants being infected for first time. Upon DNA analysis, three participants also had hybrid co-infection at this time point. At 12 months, only 6 participants had Schistosoma infection with no hybrids detected. In summary, like S. haematobium and despite praziquantel treatment, both zoonotic and hybrid schistosomes can continue to cause MGS, which pose a further tangible challenge in future management and control measures.