The larval and juvenile development was compared between Lefua echigonia and Lefua sp., both endemic and endangered species in Japan. L. echigonia larvae collected in sunny wetlands were planktonic and swam in the middle to upper layers in lentic waters, whereas L. sp. larvae swam with their abdomen facing toward the substrate along the river bottom in well shaded waters of mountain streams. Larvae and juveniles of both species have a distinct dark band on the lateral side of snout. L. echigonia larvae have melanophores on the dorsal body, gut region, and around the lateral midline, whereas melanophores distribute broadly on the body in L. sp. larvae. Eyes are located more dorsally in larvae of L. sp.: in the ventral view of the head, the eyes of L. echigonia larvae could be seen, but those of L. sp. larvae could not be seen. L. echigonia larvae and juveniles have relatively large eyes and eye diameters were larger than the snout lengths. Lefua sp. larvae and juveniles have relatively small eyes and eye diameters were smaller than the snout lengths. These characters of melanophore distribution, eye size, and eye location are concluded to show adaptation for each habitat.