Following the bleaching events of 1998 and 2001, Seriatopora hystrix disappeared from shallow reefs around Okinawa Island, Japan (van Woesik et al. 2011). Here we report finding S. hystrix in a mesophotic coral ecosystem near Motobu Peninsula on Okinawa Island. This diverse coral community occurs on the reef downslope from ~35 m and extends to at least 47 m depth, with the lower boundary yet to be defined. Along with Acropora tenella (Fig. 1) and Pachyseris speciosa (Fig. 2), S. hystrix (Fig. 3) is one of the most abundant species in this community. Following the “extinction” of shallow S. hystrix, no new recruitment events were observed in nearby shallow reefs; thus, the presence of a deep population of this species likely does not originate in recent recruitment but would demonstrate that S. hystrix has not gone extinct in this location. Potentially, this deep population could contribute to the recolonization of S. hystrix at shallower depths, although that is strongly dependent on the level of genetic structuring over depth (Bongaerts et al. 2011; van Oppen et al. 2011). The importance of other “shallow” species in community composition is being further investigated to determine the possible role of this reef as refugium.