A population of the mud shrimp, Upogebia major, inhabiting Kasaoka Inlet had a higher frequency of intersex males compared to other populations in the Seto Inland Sea, Japan. This population also featured a high prevalence of the branchial epicaridean parasite, Gyge ovalis, and inhabited a tidal flat characterized by increasingly softer sediments going into the lower tidal areas. We examined the rates at which infection co-occurred with intersex features and checked whether infection patterns varied with intersex occurrence according to host size and tidal level position. Fewer specimens were both intersex and infected than those having only one of either condition; infection was not a significant predictor of intersex. However, infection in young hosts that recovered from the parasite could be associated with the intersex morphologies and account for the majority of cases that were intersex but parasite-free. Deletions of the cuticular ridge (CRD) between the first and second abdominal segment and tidal level position were correlated with intersex. Lower tidal zone mud shrimp were, respectively, three and four times more likely to be intersex and exhibit CRD than those in the upper tidal zone. Potentially inclusive factors that may influence these trends are higher rates of early infection and increased exposure to sediment-bound pollutants in mud shrimp inhabiting the lower tidal areas.