Exon-primed, intron crossing DNA markers (EPICs) were screened for Mendelian-like allele size polymorphisms in three stingray species (Himantura gerrardi, Neotrygon kuhlii and Taeniura lymna) from the central Indo-West Pacific, where they are commercially exploited. Four to 7 size-polymorphic intron loci were selected in a species, and were subsequently tested as genetic markers of stock structure. Sharp genetic differentiation was observed between populations within each species across the Indo-Malay-Papua archipelago (Weir and Cockerham's ^θ-values reaching 0.153-0.557 over a few thousand km). A trend of increasing genetic differentiation with increasing geographic distance was apparent in N. kuhlii, in which populations distant by 3,000 km were differentiated by an estimated ^θ ~ 0.375. This value was an order of magnitude higher than usually reported in coastal benthic teleost fishes and indicates strong sub-population structure. This is likely, at least partly, a consequence of the sedentary benthic habits of N. kuhlii at all life stages. Because replenishment of overexploited populations of N. kuhlii and two other stingray species from the central Indo-West Pacific is unlikely at ecological timescales, management should be planned at the local geographic scale.