Coral reef ecosystems are now severely threatened by anthropogenic stresses including climate change. In 1998 and 2001, most shallow Scleractinia corals such as Seriatopora hystrix went locally extinct due to high seawater temperature in Okinawa. However, healthy S. hystrix populations were reported at a nearby upper mesophotic site (40 m depth) in the recent years. Such mesophotic coral ecosystems may release larvae that help the recovery of nearby shallow populations. This study aims to elucidate if mesophotic habitats can supply larvae to shallow habitat for recovery. In this study, we collected 393 S. hystrix samples from different depths (1 to 73 m) in the Ryukyu Islands. We applied a genome-wide SNP analysis called MIG-seq to examine their genetic structure. STRUCTURE analysis first indicated at least three hidden clade (named x, y, and z clade) that are not correlated with depth or geographic distance along with the Ryukyu Islands. Further analysis within each clade revealed additional two lineages each that are basically found in either deep or shallow. However, one of the two lineages in y clade was found both deep and shallow water implying genetic exchange between shallow and deep populations.