Worldwide decline has been observed in coral populations due to environmental changes at both regional and global levels. Since corals have a typical metapopulation structure, the recovery of severely disturbed local populations depends on larval recruitment from outside the disturbed region. Therefore, the connectivity among local populations may play a key role in the disturbance/ recovery dynamics of coral populations. On the basis of the simulation of surface currents, derived from ocean currents, we hypothesized that the genetic connectivity of coral populations is weak between the northern and southern regions of Sekisei Reef, Japan. To test this hypothesis, the connectivity of the population of the broadcast-spawning coral Acropora digitifera, one of the dominant corals in the Sekisei Reef, was analyzed at six sampling sites that were 5–25 km apart by using six microsatellite markers. The degree of genetic differentiation of A. digitifera was very low among all the sites (FST from -0.006 to 0.015), and no evidence was found in support of our hypothesis. The relative lack of genetic differentiation of A. digitifera among the sites may be attributable to the large effect of wind-driven surface currents, which highly vary on an annual basis, on coral larvae or to the time gap between simulation based on ocean current patterns and accumulation of genetic differences. Considering the pattern of the genetic connectivity of A. digitifera in the Sekisei Reef, the sites that are located within less-disturbed areas may act as larval sources and should, therefore, be preserved.