The high-mountain lakes on the Yungui Plateau in China are exposed to high-intensity ultraviolet radiation, and contain low concentrations of chromophoric dissolved organic matter (CDOM). We determined CDOM absorption, fluorescence, composition, and source in 38 lakes on the Yungui Plateau at altitudes of 1516 to 4591 m above sea level. Total nitrogen (TN), total phosphorus (TP), and chlorophyll a (Chl a) concentrations significantly increased with increasing trophic state, and decreased with altitude. The CDOMabsorption coefficient aCDOM(280) significantly increased with increasing trophic state, but not with altitude. There were significant and negative correlations between altitude and TN, TP, Chl a concentrations, and aCDOM(280). Parallel factor analysis identified two humic-like and two protein-like fluorescent components. Humic-like component 1 was terrestrially derived and positively correlated to CDOM absorption. Component 2 was similar to a marine humic-like substance originating from biological degradation of phytoplankton. Components 3 and 4 were autochthonous tryptophanlike and tyrosine-like fluorophores.CDOMwas, thus, a mixture of material from the catchment and autochthonous material produced by biota in the lake. CDOM fluorescence characteristics of oligotrophic and mesotrophic lakes were dominated by the spectral signatures of protein-like components, but marine and terrestrial humic-like components dominated in eutrophic lakes. The fluorescence indices FI255, FI310, and FI370 were useful tools for readily defining and classifying CDOM characteristics in the Yungui Plateau lake waters.