A variety of fish species undergo an ontogenetic change in prey selectivity, and several potentially interacting factors, including nutrient requirement, microhabitat change, and foraging ability, may account for the occurrence of the shift. Here we examine the foraging ecology and ontogenetic diet shift of a micro-carnivorous goby, Pterogobius elapoides (serpentine goby), dominant component of fish assemblage in shallow rocky areas off the coast in Korea and Japan. Although most other gobies are primarily benthic carnivores, P. elapoides is a semipelagic fish; however, little is known about how those species change their foraging tactics with growth. In our diet analyses, the most common diet was pelagic copepods and benthic amphipods, and diet shift was observed from pelagic to benthic with growth. The ontogenetic diet shift seems to be the result of the preference for energetically more profitable prey in larger-size classes as well as the results of different prey availability due to among-habitat variation in diet. However, differential food preference does not appear to affect individual scope for searching food. Several factors such as predation pressures and interspecific resource partitioning might contribute to the changes in diet observed among size classes, which were included in our ongoing tests.