Spatial distribution is variable among species on different spatial scales, with many abiotic and biotic factors affecting habitat selection. The effect of substrate traits on species distributions has long been studied but many aspects still remain poorly understood. While larvae of some holothurians are known to settle depending on water temperature, light preference, etc, it is unclear how adults choose their habitats and form patches. We investigated habitat selection in an intertidal sea cucumber, Polycheira fusca, through laboratory experiments in which conditions of light (light/shade) and substrate colour (white/black) were manipulated. Our experiments revealed that P. fusca tended to stay in the shaded area, and on a black-coloured substrate. It was found that light and colour greatly affected their distribution in patches. One possible reason why P. fusca tended to stay more in shaded areas is that the differences in light conditions might create variation in water temperature and could influence the metabolism of P. fusca. Substrate colour may affect P. fusca distribution by functioning as camouflage for them, or P. fusca may be attracted to certain sand particles that give darker colour to the substrate.