Several mechanisms of fish ontogenetic dietary shifts, which have important ecological implications, have been proposed. We studied the mechanism of dietary shifts of a benthophagous fish Goniistius zonatus, focusing on the effect of foraging on calcareous algal mat, one of its main feeding substrates, through comparison between two local populations (Morode and Arakashi) with different feeding ecology. The studied fish (11–29 cm SL) fed on various kinds of small invertebrates inhabiting the substrates, using a suctorial feeding mode without visual discrimination towards individual prey. At Morode, gut contents of small fish consisted of more epifaunal and less infaunal organisms than those of large fish, that is, mainly small crustaceans in small fish, and many invertebrates other than crustaceans in large fish. By contrast, at Arakashi, gut contents consisted mostly of epifaunal crustaceans regardless of fish size, i.e., fish showing no dietary shifts. At Morode, G. zonatus took foods mostly from thick calcareous algal mat, whereas fish foraged mainly on thin algal mat and bare rocks at Arakashi, the difference being due to the local differences in the substrate component. The algal mat of Morode harbored much larger amount of infaunal animals than any substrates of Arakashi. At Morode, large fish more forcefully and deeply thrust the mouth into thick algal mat than small fish, and was likely to suck up more infaunal prey using great suctorial force. The comparison clearly indicates that the dietary shifts of G. zonatus at Morode resulted from size-related efficiency in straining foods from heterogeneous micro-topography of thick algal mat.