Coral reproduction is vital for reef recovery. Corals reproduce by releasing gametes or larvae into the water column. Successful recruitment depends on the ability of larvae to find suitable habitats for permanent attachment to the reef substrate (settlement) since this determines the survival rate after transformation (metamorphosis) into sessile polyps. Larvae follow environmental cues to appropriate settlement spots. While most research on coral settlement has focused on the identification of natural settlement cues, the cellular structures used by larvae to sense these cues are still largely unknown. This study investigated the receptors responsible for settlement of the stony coral Acropora millepora based on five assumptions regarding the spatial and temporal expression and their phylogenetic distribution by combining the methods of proteomics, transcriptomics, phylogenetics and pharmacological settlement assays. For example, the receptors that receive settlement cues are assumed to be present in ciliary membranes of competent larvae and absent in pre-competent stages. On this basis, mass spectrometry techniques were used to investigate changes in protein composition between pre-competent and competent larvae in membrane samples of isolated cilia. Furthermore, the settlement receptors are predicted to be present at the aboral larval part because this is the region that probes and attaches to the substratum. Therefore, transcriptomics was applied to investigate gene expression differences between aboral and oral larval parts. The application of this multi-omics approach resulted in the shortlisting of nine settlement receptor candidates. These candidate receptors represent promising leads to develop treatments to increase settlement efficiency for coral aquaculture.