Abstract The growth and distribution of the two mangrove seedling species, Avicennia marina (Forsk.) Vierh. and Rhizophora stylosa Griff., were studied in the low-shore zone at three locations along two estuaries of Darwin Harbour to determine how growth varied along the estuary and within the habitats of the low shore zone. The low shore environment was heterogenous for factors such as salinity and light, with substantial variation within and between locations. Seedlings of Avicennia were in higher densities in light gaps than in the adjacent forest, and density in both habitats decreased towards the mouth of the estuary. Growth of Avicennia seedlings, as measured through in situ growth trials and plant harvests, increased towards the mouth of the estuary. Results for Rhizophora seedlings were more complex although some similar trends were evident. This may have been due to the greater early survival of Rhizophora seedlings compared to Avicennia seedlings. The importance of propagule origin was investigated, for Rhizophora, by transplanting propagules between locations along one estuary. Increased seedling survival was observed at the propagule source site; however, this effect was subtle and probably not the most important factor affecting seedling survival at a site.