Hydrolithon murakoshii sp. nov. (Rhodophyta, Corallinaceae, subfamily Mastophoroideae) inhabits well-illuminated, flat substrata from the reef edge to the shallow fore-reef (< 5 m deep) on Ishigaki-jima, Ryukyu Islands, southwestern Japan. The species is epilithic, encrusting, and yellowish brown to pale orange with a microscopically tessellate surface. Trichocytes occur singly at the thallus surface or in vertical columns that become buried in the thallus. Cells surrounding pore canals of mature tetrasporangial conceptacles are well stained and distinctly vertically elongate (narrowly ovate in sections). In marked contrast to its rarity and limited occurrence in the present-day reefs on the Ryukyus, H. murakoshii occurs commonly in middle Pleistocene reef limestone which is thought to have been deposited at depths up to 35 m.