Larval settlement and metamorphosis of many estuarine decapod crustaceans are triggered by environmental cues and chemical substances produced by the conspecific population. Here, we examined the influence of substrata and conspecific cues on the stimulation of the megalopal stage of the burrowing ghost shrimp (Lepidophthalmus siriboia) in the following five treatments: (1) adult-conditioned seawater (ACSW), (2) filtered seawater (FSW) + sand, (3) FSW + muddy sand (MS), (4) ACSW + MS and (5) FSW without cues (control). All megalopae settled and exhibited burrowing behaviour in the treatments containing substratum. The percentage of metamorphosis to juvenile was high (=96%) in all treatments. Megalopae developed significantly faster in the control (5.7 days, ±0.9 s.d.) than in the remaining treatments (6.8–7.3 days). These findings demonstrated that settlement of L. siriboia megalopae is strongly induced by substrata, whereas their metamorphosis occurs irrespective of the presence or type of exogenous cues associated with estuarine habitat and conspecific adults. This suggests certain flexibility concerning the ontogenetic stage at which recruitment to the benthos occurs. The independence of metamorphic inducers should be important for colonisation of new estuarine areas as well as for recovery and maintenance of viable populations in disturbed habitats where callianassid ghost shrimps are heavily exploited.