Abstract The nursery habitats of flatfishes range from offshore areas to rivers, with salinity conditions varying significantly between the habitats selected by larvae and juveniles. Morphological characteristics of larvae also contribute to the successful recruitment to specific nursery areas. In the present study, ontogenetic developments of low-salinity tolerance and morphology of five pleuronectid flatfishes were examined, and compared with their previously described ontogenetic migrations. Species examined were starry flounder Platichthys stellatus, stone flounder Platichthys bicoloratus, spotted halibut Verasper variegatus, marbled flounder Pseudopleuronectes yokohamae and slime flounder Microstomus achne. The first three were categorised as ‘cross-shelf species’, marbled flounder as ‘demersal-egg species’ and slime flounder as ‘offshore species’. Their typical nurseries were rivers, estuaries, tidal flats, coastal areas and offshore areas, respectively. Low-salinity tolerance from hatching to juvenile stage was examined by survival 48 h after transfer (A to I stage) and seven days after transfer (I stage) from seawater to various salinities (0, 1, 2, 4, 8, 16 and 32 ppt). High survival in 4 ppt was found in all yolk-sac larvae, but decreased in mid-larval development. During metamorphosis, starry flounder, stone flounder and spotted halibut developed strong low-salinity tolerance and juveniles were able to survive in 0, 1 and 2 ppt, respectively. In contrast, marbled flounder and slime flounder did not show these clear developments and juveniles could only survive in 4 and 8 ppt, respectively. In the morphological development, differences in standard length (SL) and relative body depth (BD) to SL (%BD/SL, an indicator of locomotive adaptation of flatfish larvae showing tilt swimming behaviour during the eye translocation) increased with larval development, and the greatest SL and %BD/SL were observed at the metamorphic climax H stage in the order of slime flounder (24.0 mm, 61.7% at 110 days after hatching, DAH), spotted halibut (14.5 mm, 42.1% at 50 DAH), stone flounder (9.5 mm, 41.1% at 34 DAH), starry flounder (7.0 mm, 34.8% at 28 DAH) and marbled flounder (6.9 mm, 28.5% at 24 DAH). ‘Cross-shelf species’ are characterised by strong inshore migration and settlement in shallower nurseries, ‘demersal-egg species' by a small habitat shift from coastal spawning to nursery areas with faster settlement of larvae with small size and slender shape, and ‘offshore species’ are characterised by gradual settlement in deep areas by locomotive adaptations of larvae with a large body surface area. So the development of low-salinity tolerance and morphology closely reflect the known ontogenetic migrations of the five species along the nearshore-offshore gradients. Especially, inverse relationships between low-salinity tolerance and metamorphic size in the three cross-shelf species, together with the general patterns of lower predator densities in lower salinity environments, suggest that low-salinity adaptability is critical for the survival strategy of species using shallow, nearshore areas as nurseries.