Plant cell wall polysaccharides undergo a slower degradation process in deep subsoil layers than in topsoil. Through the identification of organic compounds in subsoil, we may gain an understanding of this degradation process. In the present study, we extracted alkali-soluble polysaccharides from subsoil bore samples at depths of 5, 18, 29, 35 and 40–43 m, and performed sugar composition and sugar linkage analyses. Based on the results, we suggest that cellulose, arabinoxylan, mannan and pectic polysaccharides derived from plant cell walls and β-1,3-glucan and/or β-1,3:1,6-glucan from fungal cell walls exist in deep subsoil layers.