Some characteristics of germ cell differntiations during spermiogenesis and mature sperm ultrastructure in male Phacosoma japonicus were investigated by transmission electron microscope observations. The morphology of the spermatozoon of this species has a primitive type and is similar to those of other species in the subclass Heterodonta. Morphologies of the sperm nucleus and the acrosome of this species are the cylindrical type and cap shape, respectively. The spermatozoon is approximately 45-50 ${mu}m$ in length, including a long curved sperm nucleus (about $3.70{mu}m$ long with 45 $^{circ}$ of the angle of the nucleus, an acrosome (about $0.55{mu}m$ in length), and tail flagellum (about 42-$47{mu}m$)The axoneme of the sperm tail shows a 9+2 structure. As some characteristics of the acrosomal vesicle structures, the basal and lateral parts of basal rings show electron opaque part (region), while the anterior apex part of the acrosomal vesicle shows electron lucent part (region). These characteristics of the acrosomal vesicle were found in the family Veneridae and other several families in the subclass Heterodonta. These common characteristics of the acrosomal vesicle in the subclass Heterodonta can be used for phylogenetic and systematic analysis as a taxonomic key or a significant tool. The number of mitochondria in the sperm midpiece of this species are four, as one of common characteristics appear in most species in the family Veneridae and other families in the subclass Heterodonta. However, exceptionally, only three species in Veneridae of the subclass Heterodonta contain 5 mitochondria. The number of mitochondria in the sperm midpiece can be used for the taxonomic analysis of the family or superfamily levels as a systematic key or tools.