Megalopae of several crab species exhibit active habitat selection when settling. These megalopae usually select structurally complex habitats which can provide refuge and food. The portunid mud crab, Scylla serrata, is commonly found within the muddy estuaries of the Indo-West Pacific after attaining a carapace width >40 mm. Despite substantial efforts, the recruitment mechanism of juvenile mud crabs to estuaries is not understood because their megalopae and early stage crablets (carapace width <30 mm) are rarely found. We used laboratory experiments to determine whether megalopae and early stage crablets are selective among three estuarine habitats which commonly occur in Queensland, Australia. These animals were placed in arenas where they had a choice of habitats: seagrass, mud or sand, and arenas where they had no choice. Contrary to the associations exhibited by other portunid crab megalopae, S. serrata megalopae were not selective among these estuarine habitats, suggesting that they tend not to encounter these habitats, or, gain no advantage by selecting one over the others. The crablets, however, strongly selected seagrass, suggesting that residing within seagrass is beneficial to the crablets and likely increases survival. This supports the model that for S. serrata, crablets and not megalopae tend to colonise estuaries, since a selective behaviour has evolved within crablets but not megalopae.