It is essential to consider genetic composition for both conventional coral restoration management and for expanding new interventions to counter the significant global decline in living corals. Population genetic structure at fine spatial scale should be carefully evaluated before implementing strategies to achieve self-sustaining ecosystems via coral restoration. Here, we investigated the population genetic structure of two acroporid species at Kume Island, Okinawa, Japan. 140 colonies of Acropora digitifera from 7 study sites, and 81 colonies of Acropora tenuis from 6 sites were collected. We obtained 384 SNP loci for A. digitifera and 470 SNPs for A. tenuis using a comparatively economical technique, Multiplexed ISSR Genotyping by sequencing (MIG-seq). Observed heterozygosity was significantly lower than expected heterozygosity at all SNP sites in both acroporid species, suggesting deficient genetic diversity possibly caused by past massive coral bleaching. Even though both species are broadcast spawners, we found different population structure in the two species. No detectable structure was evident in A. digitifera, but two distinct clades were found in A. tenuis. The genetic homogeneity of A. digitifera at Kume Island suggests that this species could be used as focal species for active restoration in terms of genetic differentiation at this island. On the other hand, A. tenuis unexpectedly included two distinct clades with no or little admixture within a small spatial study area, possibly representing two reproductively isolated cryptic species. Thus, when using A. tenuis, it would be prudent to avoid disturbing genetic composition of wild populations until this question is answered.