With a focus on building an inventory of subtropical species of epifaunal holothurians and completing an environmental assessment, SCUBA surveys were carried out in the Amami Islands of Kagoshima Prefecture in southern Japan. The following 12 nominal species belonging to seven genera (subgenera), as well as two as yet undescribed species belonging to two genera, were observed: Bohadschia argus Jäger, 1833; B. bivittata Mitsukuri, 1912; B. vitiensis (Semper, 1867); Holothuria (Halodeima) atra Jäger, 1833; H.(H.) edulis Lesson, 1830; Holothuria (Microthele) nobilis (Selenka, 1867); Personothuria graeffei (Semper, 1867); Stichopus chloronotus Brandt, 1835; S. hermanni Semper, 1867; S. naso Semper, 1867; Thelenota anax H.L. Clark, 1921; Euapta sp.; Synapta maculata (Chamisso et Eysenhardt, 1821); and Opheodesoma sp. In the semi-closed waters around the Amami Islands, epifaunal holothurians showed what seemed to be species-specific distribution patterns related to topographical features. Furthermore, ignition loss values of feces and sediments suggested that selective deposit feeding may be predominant in at least several of the species sampled.