Putative sites of bone resorption in the acellular bony skeleton of the medaka fish (Oryzias latipes) were investigated primarily by RNA in situ hybridization and histological analysis. Numerous cells that displayed intense enzymatic activity of tartrate-resistant acid phosphatase (TRAP), the main marker of osteoclasts, were distributed in the pharyngeal region of this fish. Moreover, these cells expressed cathepsin K, an osteoclast-specific gene, as well as the genes for TRAP and vacuolar-type proton ATPase (V-ATPase). Some of the TRAP-positive cells displayed all of the morphological characteristics equivalent to those of mammalian- and bird-type osteoclasts. These cells were associated primarily with the shedding teeth and their supporting bones (pedicles), where alkaline phosphatase (ALPase)-positive osteoblasts were also located, implying progressive bone remodeling associated with tooth replacement in these regions. In contrast, the inner aspects of the neural and hemal arches of the vertebral column, which were the only sites of bone resorption other than the tooth-bearing bones, showed sporadically aligned flat mononuclear TRAP-positive cells without a ruffled border, indicating a different mode of bone remodeling in these regions. These results suggest the feasibility of medaka as a model animal for the investigation of bone-related abnormalities and their genetic backgrounds.