The sandfish Holothuria scabra is one of the most widely-traded and in-demand sea cucumber species, with the dried form commanding steep prices in global markets. In the Philippines, the species is considered overharvested with declining capture production. D elineation of genetic stocks is important to guide the development of sustainable management and conservation interventions. This study used a genotyping-by-sequencing approach based on doubl e-digest restriction site associated DNA sequencing (ddRADseq), to assess regional and fine-scale genetic structure of Philippine populations of H. scabra . Sandfish were sampled from 14 natural populations across the Philippine archipelago. Population genomic analysis of 163 individuals genotypes at 3,646 single-nucleotide polymorphism (SNP) markers reveals significant genetic differentiation (overall FST = 0.0342, p < 0.05). Across broad spatial scales, patterns of genetic structure were broadly concordant with marine biogeographic regions. G enetic structure was further detected within regions, indicating that gene flow and dispersal of sandfish may be limited even at smaller spatial scales (< 200 kms). Outlier loci analysis also suggests that some genetic clusters may be under local, adaptive selection warranting further investigation . These findings provide insights on sea cucumber stock boundaries and present baseline information useful for establishing spatially-explicit fishery resource management strategies.