A sediment core from Lake Koucha (eastern Tibetan Plateau) was investigated using organic biomarkers and their stable carbon isotope signatures. The correlation between TOC content, total amount of aquatic macrophyte-derived n-alkanes (e.g. nC23) and δ13C values of TOC and nC23 indicates that Lake Koucha was macrophyte-dominated before 8 cal ka BP. Shortly after the lake turned from a saline to a freshwater system at 7.2 cal ka BP, a variety of algal and bacterial markers such as hopanoids and isoprenoids emerged, of which phytane, pentamethylicosene (PMI), moretene and diploptene are particularly abundant. Phytane and PMI show different isotopic signals (≈-18 and ≈-28‰, respectively), which indicates that they originated from different sources. Phytane may have been derived from cyanobacteria, while methanogenic archaea may be the source of PMI. The isotopic depletion of diploptene and moretene (≈-60‰) indicates the presence of methanotrophs. After 6.1 cal ka BP, the saturated C20 highly branched isoprenoid (HBI) became the dominant constituent of the aliphatic hydrocarbon fraction. Such dominance has rarely been reported in lacustrine environments, and indicates a strong presence of algae (most likely diatoms) or cyanobacteria. At 4.7 cal ka BP, the appearance of an unsaturated C25 HBI, which is a specific biomarker for diatoms, was noted. Furthermore, the level of nC17-alkane was observed to increase in abundance in the uppermost two samples. These results suggest that the lake was phytoplankton-dominated during the last 6.1 ka. Relatively low biomarker concentrations and δ13C values at 6.0, 3.1 and 1.8 cal ka BP indicate the occurrence of cool periods, which is in agreement with inferences from other locations on the Tibetan Plateau. The δ13C values of nC23 range from -23.5 to -12.6‰, with high values at the peak of macrophyte abundance at ca. 11 cal ka BP and at the phytoplankton maximum between ca 6.1 and 2.8 cal ka BP. Thus, aquatic macrophyte-derived mid-chain n-alkanes have been found to be excellent indicators of carbon-limiting conditions, which lead to the assimilation of isotopically-enriched carbon species. The limitation of carbon sources could be a localized phenomenon occurring in dense plant stands (as in the older section of the core), or it may be induced by high primary productivity (as in the younger section). Since the δ13C value of the inorganic carbon source may vary, the offset between the δ13C values of nC23 and TIC could serve as a more precise proxy for carbon-limiting conditions in lacustrine environments, which could in turn be interpreted with respect to lacustrine paleo-productivity. © 2009 Springer Science+Business Media B.V.