Broadcast-spawning corals expel eggs and sperm, and the fertilized eggs develop into planulae in the water column. As these sessile corals generally disperse during the planktonic larval stage, their larval characteristics (e.g., survival and settlement rates) are thought to be important for their dispersal. Although some studies of coral larval dispersal have focused on the maximum time that larvae can remain viable and settle, the relevance of this maximum settlement competency period for long distance dispersal remains unclear. To examine the relationship between competency periods and genetic differentiation, we performed laboratory experiments to investigate settlement rates of planulae and determine the degree of genetic differentiation in Acropora digitifera in the Ryukyu Archipelago, southern Japan. In addition, we compared our findings to published data for A. tenuis, which was studied using our methods. Our results indicated that the maximum settlement competency period was lower in A. digitifera planulae (54 days) than in A. tenuis (69 days) planulae. The mean survival rates at 45 days and 59 days after spawning were less than 10%. Furthermore, percentages of planulae that remained viable and settle at 30 days after spawning (survival rate × settlement rates at 30 days) were approximately 18% and 25% in A. digitifera and A. tenuis, respectively. By contrast, gene flow (Nem: number of migrations per generation) was significantly higher in A. digitifera (7.8 to 41.4) than in A. tenuis (3.1 to 22.5). These results indicate that the settlement competency period and survival rates are unlikely to be robust predictors of gene flow. Overall, we detected significant genetic differentiation between Kerama and Okinawa in A. digitifera. As direct observation of planula dispersal between Kerama and Okinawa has been reported, we concluded that genetic mixing is not complete, but that some localized planulae may disperse from Kerama to Okinawa via a specific current depending on reef or locality.