To better understand the habitat choices of Japanese sea cucumber Apostichopus japonicus juveniles, we investigated their responses to various stimuli. Specifically, their phototactic, thigmotactic, and geotactic responses were tested by placing sea cucumber juveniles in appropriately designed test tanks, while their responses to turbulence were tested in tanks in the presence or absence of wind-driven waves. Sea cucumber juveniles showed clear negative phototaxis, but there was no clear evidence of thigmotaxis or geotaxis. The juveniles frequently appeared at the surface of the water in a tank lacking turbulence, but much less frequently in a tank with turbulence. We conclude that sea cucumber juveniles choose their habitat via a combination of phototaxis and their limited ability to attach to hard substrates.