Hydrothermal treatment was used to study the separation of lignin from bark derived from biomass. A coupled-system of two batch reactors was used to treat Japanese cedar bark (ca. 45% lignin) with water at 473 K-573 K without additives and to collect lignin fractions at given times. Hydrothermal treatment of bark at a temperature of 548 K and a treatment time of 10 min allowed 65 wt% of the lignin to be separated, which means that it is possible to obtain about 0.3 kg-lignin per kilogram of Japanese cedar bark. From the characterization, it was revealed that the hydrothermal-soluble lignin had a simple structure with a molecular mass of about 1000 Da. The yield of lignin decreased for treatment temperatures higher than 548 K that is attributed to carbonization. Hydrothermal treatment of bark can be used to recover lignin and has potential application to biorefineries.