Organic geochemical study on an extremely acid crater lake (Yugama, pH = 1.2) of an active Kusatsu-Shirane Volcano in Japan has been carried out to clarify the features and sources of organic components in relation to biological activity. Generally, n-alkanes ranging from n-C15 to n-C36 with a predominance of long-chain (n-C20–n-C36) n-alkanes maximizing at n-C27, n-C29 or n-C31 were detected in suspended solids (≥0.60 μm), sulfur aggregate and surface sediments of the lake, and soils in the surroundings of the lake, together with pristane, phytane, squalane, steranes and/or triterpanes. A series of n-alkanoic acids ranging from n-C8 to n-C32 with a predominance of even-carbon numbers were found in all the samples, along with cis- and trans-isomers of n-alkenoic acids [n-C16:1 (Δ7 and δ9) and n-C18:1 (Δ9 and Δ11)], iso- and anteiso-alkanoic acids (C14–C17), and cyclopropyl alkanoic acids (C17 and C19). No polyenoic alkenoic acids were, however, found in all the samples. Normal 3-hydroxy acids (n-C10–n-C18) mainly maximizing at n-C14 were detected, together with iso- and anteiso-3-hydroxy acids (C12–C18). The features of organic components in the lake waters and sediments indicate that they can be attributed to bacteria, such as Thiobacillus thiooxidans in addition to certain uncultured bacteria, with some influences of eroded, and/or wind-transported materials containing vascular plant debris from the surroundings of the lake. Low concentrations of fatty acids mainly reflect the paucity of photosynthetic producers and small living biomass in the lake. Relatively high trans/cis-C16:1 alkenoic acid ratios (0.24–0.52) may be caused by unfavorable habitat for microbial activity in the lake. The thermal maturation parameters of (20S/20R)-24-ethyl-5α(H), 14α(H), -17α(H)-cholestane ratios (0.49–0.77) and (22S/22R)-17α(H), 21β(H)-30-homohopane ratios (1.0–1.4) have not reached equilibrium values, but may have been significantly influenced by hydrothermal activity in the past in Lake Yugama and the surroundings of the lake.