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Habitat recognition and selective settlement by dispersive propagules greatly increases the post-settlement survival chances of sessile organisms. To better understand the key role some species can play in the structure of highly complex coral reef ecosystems, we compare the role of two independent, but sequential, processes: settlement choice and post-settlement survival. This study describes the chemical and physical recognition and ranking of specific settlement substrata by coral larvae. Several species of crustose coralline algae (CCA) are known to induce coral settlement; however they also employ physical and biological anti-settlement defense strategies that vary greatly in effectiveness. We examine the interactions between settling larvae of two common reef building coral species (Acropora tenuis and A. millepora) and five species of CCA (Neogoniolithon fosliei, Porolithon onkodes, Hydrolithon reinboldii, Titanoderma prototypum, and Lithoporella melobesioides) that co-occur on reef crests and slopes of the Great Barrier Reef, Australia. Distinct settlement patterns were observed when coral larvae were provided with a choice of settlement substrata. Settlement on the most preferred substratum, the CCA species T. prototypum, was 15 times higher than on N. fosliei, the least preferred substratum. The rates of post-settlement survival of the corals also varied between CCA species in response to their anti-settlement strategies (shedding of surface cell layers, overgrowth, and potential chemical deterrents). Rates of larval settlement, post-settlement survival, and the sensitivity of larvae to chemical extracts of CCA were all positively correlated across the five species of CCA. Nonliving settlement substrata on coral reefs is sparse; consequently the fact that only a few CCA species (notably T. prototypum) facilitate coral recruitment, has important implications for structuring the reef ecosystem.