Japanese species of the genus Intybia are revised taxonomically, with the examination of the endophallic structure. Eight species, including one new species Intybia donan sp. nov. from Yonaguni-jima, are recognized. All species are described or redescribed with a key and figures. The endophallic structure contains one primary sclerite (gonoporal piece), three secondary sclerites (ligula, semi-gonoporal piece, and spinous plate) in some species, and a membranous basal area densely covered with many spines (spinous area). Based on the structures of the endophallus, the Japanese members of the genus are divided into two species groups (the histrio and pelegrini groups). The pelegrini species group is furthermore subdivided into three subgroups (subgroups 1–3). New distributional records are as follows: I. histrio from Hachijô-jima and Tanega-shima; I. niponica from Sakhalin and I. takaraensis from Tokuno-shima and Amami-Ôshima.
Taxonomy, endophallus, new species, species group, distribution.