Population genetics analyses should be considered when releasing hatchery-produced juveniles of the sea cucumber Holothuria scabra when spawners from nonlocal populations are used. In New Caledonia, within-region genetic heterogeneity of H. scabra populations (examined through allozyme electrophoresis of 258 animals) indicated high gene flow between nine sites and F_ST values dOld_ID not deviate significantly from zero. However, exact tests indicated that populations at two sites with limited water exchange in the southern location were significantly different from populations at three other locations on the west coast. Inclusion of H. scabra sampled in Bali (n = 90) and Knocker Bay, Australia (n = 47), and comparisons with existing data from the west Pacific (Torres Strait, Solomon Islands, Upstart Bay, Hervey Bay) showed that populations were significantly different (using exact tests) and samples partitioned distinctly using unweighted pair group method with arithmetic mean clustering. Rogers’ genetic distance values between populations were significantly related to geographic distances, showing a pattern of isolation by distance. The rapOld_ID increase in genetic distance over the first few hundred kilometres supports the view that the spatial extent of any translocation needs to be carefully considered on the basis of knowledge of variation in allele frequencies within the target area.