The raphe of the human penis and scrotum is considered to develop secondarily after disappearance of the initial midline seam by fusion of the bilateral genital folds. However, the fetal development was still obscure. We examined histological sections of 30 fetuses (17 males and 13 females) at 10–15 weeks. In male fetuses, the scrotum was not yet clearly identified because of no descent of testis. The perineal raphe was thin and wavy at 10 weeks, and it was continuous with and took a direction same as the inferior wall of the closed penile urethra after physiological hypospadias. Depending on growth of the bulbospongiosus muscle and corpus spongiosus penis, the midline intermuscular septum obtained a connection to the subcutaneous wavy raphe and made the latter thick and straight at 12–15 weeks. Notably, the perineal raphe extended posteriorly to attach to the external anal sphincter. In female fetuses, an epithelial fusion occurred along a short distance at the posterior end of the vestibule. However, in front of the external anal sphincter, a large midline mesenchymal tissue from the urorectal septum did not contain a raphe-like structure. Moreover, since the bilateral bulbospongiosus muscles were separated widely by the vestibule, they did not provide a midline septum. Fetal development of the perineal raphe was accelerated by reinforcement from the muscular septum. In contrast, without such a muscular support, the female raphe could not maintain its growth even if the seed appeared at the posterior end of the vestibule.