Information on the environmental characteristics of the juvenile habitat of many deposit-feeding sea cucumber species is limited, despite most fished species exhibiting rapid localised depletion. The current study combined large and small scale surveying techniques within a New Zealand harbour to identify areas with high densities of juvenile Australostichopus mollis, a commercially valuable aspidochirote holothurian. Data from detailed surveys were used to relate densities of juveniles and adults with measures of physical habitat characteristics including depth, sediment facies type, grain size range, as well as measures of chlorophyll-a, phaeopigment, carbon and nitrogen content of surface sediment. Results revealed a highly localised distribution of juvenile A. mollis focused on one site associated with an area of high adult density. Sites of high juvenile A. mollis density were characterised by sediment qualities favouring epibenthic detritivorous deposit feeding, including high nitrogen content, high phaeopigment:chlorophyll-a ratio and small grain size. The high-density juvenile site had facies that were further characterised by the presence of large shell fragments (>10 cm length) of the horse mussel (Atrina zelandica), which may provide a unique settlement microhabitat for early juveniles. Unlike some other sea cucumber species, juvenile A. mollis shows no distinct spatial separation from adult sea cucumbers, no association with dense macroalgae and no clear preference for shallower depths than adults. Overall, the results illustrate the highly localised pattern of recruitment of this species to a widely distributed adult population, which may help to explain the lack of previous observations of juveniles in this species. These results indicate the importance of identifying and protecting what appear to be very specific juvenile habitats in deposit-feeding sea cucumbers to ensure continuing recruitment to exploited populations.