Mountain lakes are natural and remoted lentic water bodies with unique ecosystem structure housing high level of biological endemism. They are sensitive to environmental changes though most studies of the mountain lake ecosystems have been focused on the temperate region. Yet, only limited investigation has been undertaken in such ecologically important habitats in tropical/subtropical Asia. As the subtropical mountain lake ecosystems are strongly influenced by seasonal environmental perturbations, including periodic and stochastic hydrological disturbances due to heavy rainfall events, and the intense solar radiation during summer. It could be the major factor characterizing the energy basis for the lake food webs. In this study, the trophic structure and food utilization patterns of different fish consumers in two subtropical mountain lakes in Taiwan, including Lake Tsuifeng (TFL) and Lake Yuanyang (YYL) were investigated using stable carbon and nitrogen isotope analyses in association with gut content analysis. The two study lakes exhibited marked difference in riparian vegetation pattern, TFL was relatively unshaded with only sparsely distributed riparian vegetation whereas YYL was a densely shaded system with continuously distributed riparian forest. This resulted in distinct difference in the availability of different food sources to the food webs. Despite the high availability of the two most dominant allochthonous food sources including fine particulate organic matter and leaf litter in the densely shaded YYL, they were least utilized by most fish consumers. In contrast, fish consumers in the autotrophic TFL ecosystem showed strong dependence on autochthonous food sources (e.g. algae) which accounted for the major primary production supporting the food web. Our results will be further discussed.