The Japanese sea cucumber Apostichopus japonicus plays important ecological and economic roles in the coastal areas of Japan. Here, we aim to reveal the relation between habitat characteristics and density of juvenile and adult sea cucumbers in Maizuru Bay. Density of adult sea cucumbers was estimated by underwater visual surveys and bottom trawls and that of newly settled individuals by seedling collectors distributed in the bay. The physical environment of the sea bottom was evaluated from median diameter, total organic carbon, total nitrogen, carbon-to-nitrogen ratio, carbon isotope ratio, nitrogen isotope ratio, depth, slope, and distance from the coastline. Adult sea cucumber density was higher in the east side than the west side of Maizuru Bay, the former having a no-take zone for sea cucumbers. Juvenile sea cucumbers were most abundantly collected in the central part of the bay. High organic matter from the sea, short distance from the coastline, and high seabed gradient (steepness) had a positive effect on the density of adult sea cucumbers, and depth had positive effects on their body size. We suggest that sustainable management of sea cucumbers can be achieved by a combination of the establishment of no-take zones and increased protection of nursery habitats.