Information about the distribution of alleles among marine populations is critical for determining patterns of genetic connectivity that are essential in modern conservation planning. To estimate population connectivity in Singapore’s urbanised equatorial reef system, we analysed single nucleotide polymorphisms (SNPs) from two species of reef-building corals with distinct life histories. For Porites sp., a broadcast-spawning coral, we found cryptic lineages which were differentially distributed at inshore and central-offshore sites that could be attributed to contemporary surface current regimes. Near panmixia was observed for Pocillopora acuta with differentiation of colonies at the farthest site from mainland Singapore, a possible consequence of the brooding nature and relatively long pelagic larval duration of the species. Furthermore, analysis of recent gene flow showed that 60-80% of colonies in each population were non-migrants, underscoring self-recruitment as an important demographic process in this reef system. Apart from helping to enhance the management of Singapore’s coral reef ecosystems, findings here pave the way for better understanding of the evolution of marine populations in Southeast Asia.