Macroalgae underpin most temperate inshore ecosystems, but increasing macroalgal loss, fragmentation and range contractions are eroding connectivity among populations. Understanding loss, and predicting the likelihood of recovery, is dependent on knowledge of population connectivity and how it is mediated by variability in local seascapes. Although many studies of marine connectivity have focussed on influences of geographic distance on genetic structure, the contribution of intervening habitat is rarely considered. We tested the extent to which geographic separation, intervening suitable habitat (reef versus sand and open water) and local hydrodynamics (inferred from particle dispersal models) explained structuring of genetic variation at microsatellite loci in the habitat forming macroalga Lessonia corrugata. Genetic structuring was best explained by the availability of suitable intervening habitat (rocky reef) rather than by geographic separation, although biologically realistic estimates of dispersal probability also became important at smaller spatial scales. Our results indicate that ecological separation can be more influential than geographic distance on population genetic structuring, and this should be considered during the assessment of connectivity and gene flow in marine species.