Aim: Mangrove forests are among the world's most important ecosystems but are declining rapidly worldwide. Effective conservation management requires a better understanding of the patterns and drivers of gene flow across a range of spatial scales. Despite the capacity for long-distance propagule dispersal, field studies suggest that mangrove propagules tend not to disperse far from the release point, which has important implications for the impact of habitat discontinuities on gene flow. We use a comprehensive seascape genomics approach to investigate this concept in the world's most widely distributed mangrove species, Avicennia marina. Location: Twenty-one sites along 2,400 km of Western Australian coastline. Methods: We used 6,162 neutral SNP loci and a hierarchical sampling design to investigate patterns of gene flow and structuring among 21 populations of A. marina. We combined these data with GIS spatial analyses in a regression model to test the relative influence of habitat continuity and geographic distance on patterns of genetic differentiation. Results: We found a complex pattern of gene flow; broadscale isolation-by-distance, disrupted by strong genetic discontinuities that coincided with gaps in mangrove distribution. These genetic discontinuities formed seven discrete subpopulations with negligible evidence for recent migration among them. The regression model combining marine geographic distance and habitat continuity as explanatory variables best fit the data, explaining 86% of the total genetic variation. Main Conclusions: Our results validate previous assertions that propagule dispersal in A. marina is spatially limited and demonstrate that significant gaps in mangrove distribution present strong barriers to stepping-stone gene flow in this species. This reiterates that dispersive life history features cannot be assumed to lead to widespread connectivity and demonstrates that effective management of these important ecosystem builders should prioritize restoring habitat continuity and minimizing further fragmentation.