Three new species of echinoderid kinorhynchs are described from Daidokutsu, a submarine cave in Ryukyu Islands, Japan. Echinoderes gama sp. nov. is characterized by the presence of middorsal acicular spines on segments 4–8; lateroventral acicular spines on segments 7–9; lateroventral tubes on segment 5; sublateral tubes on segment 8; laterodorsal tubes on segment 10; and type-2 gland cell outlets in subdorsal and lateroventral position on segment 2. Echinoderes kajiharai sp. nov. is defined by the presence of middorsal acicular spines on segments 4, 6, 8; lateral accessory acicular spines on segment 9; lateroventral acicular spines on segments 6–8; lateroventral tubes on segments 2 and 5; midlateral tubes on segment 10; and type-2 gland cell outlets in laterodorsal position on segments 2 and 5, and subdorsal position on segments 8 and 9. Echinoderes uozumii sp. nov. is characterized by the presence of middorsal acicular spines on segments 4 and 6; lateroventral acicular spines on segments 6–9; lateroventral tubes on segments 2 and 5; sublateral tubes on segment 8; laterodorsal tubes on segment 10; type-2 gland cell outlets in subdorsal and lateral accessory position on segment 2; and blunt, short pectinate fringe teeth of primary pectinate fringe on segment 1. In addition, the Echinoderes multiporus species group including E. kajiharai sp. nov., and the Echinoderes bispinosus species group including E. uozumii sp. nov. are established. Furthermore, the distribution of the two species groups and the origin of Echinoderes species in Daidokutsu are discussed.