An important ecological driver underpinning coastal marine management is dispersal, but it has proven difficult to directly measure in this setting. The coast of Northwestern Australia provides an emerging frontier for implementing new genomic tools, which allows testing of dispersal under a management framework given its diverse and extreme environmental conditions. This study compares the genetic diversity, population structure and adaptive genetic variation of two species with different life history characteristics, from the Northern Territory to Shark bay. The first species, Stripey Snapper (Lutjanus carponotatus), a spawning fish with pelagic larval duration (PLD) of 33-37 days(d), is important to recreational, charter-based, and customary fishers in coastal waters throughout the Indo-West Pacific. We collected 1016 L. carponotatus samples at 51 locations. The second species, Millers Damselfish (Pomacentrus milleri), is a typical inshore reef dwelling fish which broods its eggs before an 18-21d PLD. We sampled 847 individuals from 29 very similar locations between the Kimberley and Shark Bay. Using genome scans consisting of >4,400 SNP loci for each species, we demonstrated significant genetic sub-division illustrated in pairwise Fst and STRUCTURE plots between the Shark Bay Bioregion in the south and all locations within the five more northern IMCRA bioregions for both species. Between the northern bioregions, there were differences between the species in the scale of population subdivision, genetic diversity and adaptive genetic variation. Of particular interest, is the relatively reduced larval dispersal for both species and greater adaptive genetic variation for only one of the species in the Kimberley, potentially created by the region’s complex bathymetry, and currents which are predominantly macro-tidal rather than along-shore. These results will be discussed in the context of long term conservation management initiatives of the unique marine environment in Northwestern Australia.