Japanese cedar (Ciyptomeria japonica) was treated with hot-compressed water and as decomposed products, the following compounds were recovered: furfural, 5-hydroxymethyl furfural, levoglucosan, lactic acid, glycolic acid, coniferyl alcohol, coniferyl aldehyde and vanillin. The impacts and fermentability of these compounds were studied on acetic acid fermentation by the co-culture of Clostridium thermocellum and Moorella thermoacetica. It was found that furfural, 5-HMF and lignin-derived products strongly limited acetic acid production by free cells. Importantly, co-immobilized C. thermocellum and M. thermoacetica expressed increased tolerance towards the decomposed products and successfully provided acetic acid corresponding to 93% of the theoretical maximum from Japanese cedar hydrolyzates.