The sea cucumber or sandfish Holothuria (Metriatyla ) scabra is a high-value commodity widely traded in dried form (bȇche-de-mer). Considered as overexploited throughout much of its distributional range, local declines have been reported for natural populations, highlighting the need for management options for the species. This study examines genetic connectivity of sandfish populations across the western Luzon coast using genome-wide single nucleotide polymorphism (SNP) markers generated from high-throughput DNA sequencing (DArT sequencing). Population genomic analysis based on 7,898 putatively neutral SNPs revealed significant genetic differentiation among populations sampled across 7 sites (FST = 0.0125, p < 0.05), indicating limited gene flow along the western Luzon coast spanning a distance of ~450 km. Multivariate and Bayesian approaches consistently identified four distinct genetic clusters concordant with geographic location. Migration networks suggest asymmetric northward gene flow across the western Luzon coast. However, genetic differentiation is not consistent with a pattern of isolation-by-distance, with the northernmost sites in the Ilocos region inferred as a potential admixture zone, serving as sink populations even from more distant southern sites. Population genomic analysis provides useful baseline information on sandfish stock structure and connectivity which are crucial for the development of resource management strategies such as stock restoration and enhancement from hatchery-produced animals, and conservation of genetic diversity, for this valuable fishery resource and aquaculture species.