The occurrence and distribution of settling and settled spotted halibut Verasper variegatus were compared with those of Japanese flounder Paralichthys olivaceus in shallow habitats around Shimabara Peninsula, western Japan, to elucidate the settlement and recruitment characteristics of spotted halibut, a rare pleuronectid flatfish in Japan. Push-net sampling conducted at nine sites in March and April 2003 collected spotted halibut from four nurseries located at eastern areas of Shimabara Peninsula in Ariake Bay; Japanese flounder were sampled from eight nurseries. Comparison of microhabitat distributions in a tidal-flat nursery during February-April in 2003-2007 revealed that metamorphosing larvae and juveniles of spotted halibut, which showed the drastic body coloration (black to brown) and behavioral changes (frequent swimming to settlement), were distributed mainly in the lower edge of the intertidal area, whereas Japanese flounder inhabited both intertidal and subtidal areas. Metamorphosing larvae of spotted halibut (12.6-16.5 mm standard length; n = 24) were collected in March when the highest densities were observed, whereas metamorphosing larvae of Japanese flounder (10.0-15.9 mm, n = 55) were observed during March-April. Our results suggest that spotted halibut has a narrower time/space window for recruitment to the specific nurseries compared with Japanese flounder. © 2012 The Japanese Society of Fisheries Science.