Some species of soft-shelled turtle have been known to use a conspicuous mass of villiform processes of the pharyngeal mucosa as an aquatic respiratory organ when staying underwater for prolonged periods, such as hibernation. Using hibernating turtles, Trionyx sinensis japonicus, the present study employed scanning electron microscopy to demonstrate for the first time the detailed morphology and distribution of these villiform processes. Two types of processes, complex and simple, could be identified. Light microscope observation of the transverse sections of the villi demonstrated a rich vascularization in the connective tissue of the villi, comprising arterioles and venules running in the core and capillaries in the periphery. Most of the capillaries were invaginated into the multilayered cuboidal epithelium. Near the tip of the villi they became swollen, forming sinusoidal capillaries. Transmission electron microscopy clarified the fine structure of the blood-water barrier, which consisted of a non-fenestrated endothelium and an attenuated epithelium that sandwiched a connective tissue with a discontinuous subendothelial and a continuous subepithelial basement lamina. The epithelium consisted of secretory cells, mitochondria-rich cells, and basal cells. The mitochondria-rich cells contained a cytoplasmic area filled with tubulovesicular elements. Based on their ultrastructural resemblance with the chloride cells in the fish and tadpole, these cells are suggested to be involved in the uptake of Na+ and Cl from fresh water for keeping ionic balance in the blood.