Understanding patterns of gene flow and processes driving genetic differentiation is important for a broad range of conservation practices. Genetic differentiation among populations is influenced by a range of spatial, oceanographic and environmental factors attributed to the seascape. Here, we applied a seascape genetic approach to populations of the seagrass Thalassia hemprichii at a fine spatial scale (~ 80km) in the Kimberley coast, Western Australia, a complex seascape with strong, multidirectional currents greatly influenced by extreme tidal ranges (up to 11m, the world’s largest tropical tides). We detected significant spatial genetic structure and asymmetric gene flow, in which meadows 12-14 km apart were less connected than ones 30-50 km apart. This pattern was significantly explained by oceanographic connectivity and differences in habitat characteristics, suggesting a combined scenario of dispersal limitation and facilitation by ocean current with local adaptation. Our findings add to the growing evidence for the key role of seascape attributes in driving spatial patterns of gene flow. Despite the seagrass potential for long distance dispersal, there was significant genetic structuring over small spatial scales highlighting the importance of implementing local-scale conservation and management measures.