Three new sea cucumbers collected in the intertidal and subtidal zone of southern Japan, Taeniogyrus mijim sp. nov., Rowedota chippiru sp. nov., and R. motoshimaensis sp. nov., are described. All three species display a small body size (approximately 10–20 mm), light body colour (primarily a transparent solid colour), and a small number of digits in their tentacles (one pair or two). They are easily distinguished from each other and from other congeners by the number of digits and by ossicle size and shape. Among these species, the state of the tooth series on the inner margin of the wheel ossicles is an important defining feature, i.e., a continuous row in Taeniogyrus but interrupted by concavities in Rowedota. Also, each tooth is sharp in T. mijim, trapezoidal in R. chippiru, and semicircular in R. motoshimaensis. The number of teeth per radiant is 7–16 (means of 10–13 in different specimens) in T. mijim, 7–15 (means 9–12) in R. chippiru, and 8–21 (means 11–19) in R. motoshimaensis. Among these three new species, only R. chippiru has thick rod ossicles in the body wall.