Normal females of the mud shrimp, Upogebia major, have a pair of pleopods on the first abdominal segment, while normal males do not. We have investigated nine populations in the Seto-Inland Sea, Japan, and found morphological disorders on the first abdominal segments of both males and females. In males, the first pleopods occurred. Morphology and arrangement of these additional pleopods were classified into four types. The pleopods of Types M-1 and M-2 were similar in structure to those of normal females. These males could be considered as de-masculinized individuals, and the occurrence of males with these morphological disorders showed local variation: while their frequency was high in two specific sites in Kasaoka Inlet (11.5% in Site 6 and 5.5% in Site 7), it was less than 3.5% in other sites. Other types had abnormal additional appendages similar to the walking legs (pereiopods) (Type M-3) or biramous leaf-like pleopods (Type M-4), but their frequency was extremely low (only 3 out of 1558 males inspected). Morphological disorders in males (Types M-1 and M-2) occurred independently of gonadal development, and did not affect the sexual characteristics as revealed by analyses of allometric growth and gonadal index. In females, morphological disorders were classified into five types: incomplete first pleopods (Type F-1); lack of the first pleopods (Type F-2 and F-3); transformation into the pereiopod-like pleopods (Type F-4); and biramous leaf-like pleopods (Type F-5). The frequency of Types 1–3 was especially high in Site 6 in Kasaoka Inlet (24.4%), but was less than 9.4% in other sites. A feature was that cuticular lesions often co-occurred with the morphological disorders. Possible causal factors of these abnormalities are discussed.