Southwest China, which includes the eastern margin of Tibet, is a hotspot of global biodiversity research. Previous studies showed rapid ecological change in this region, due to global environmental forcing, most notably landcover change and Nr deposition. In this study, two alpine glacier lakes, one is Jiren Lake ( 29°43'19"N, 100°48'56〃E), located above the modern treeline(altitude ca. 4480 m a.s.l.) , from Yajiang County, Garze tibetan autonomous prefecture, in Western Sichuan Plateau, and the other Lake Cuoqia(27024'13"N, 99046'18〃E), lies below the modern treeline (altitude ca. 3980 m a. s. 1.), from Shangri-La City, Diqing Tibetan Autonomous prefecture, in northwest Yunnan Province, are selected. All lakes are deep (of maximum water depth about 27 m), small and oligotrophic. A 48 cm long sediment core was taken from the center of Cuoqia Lake using UWITEC sediment corer(diameter is 60 mm) in 2012, and divided by 1 cm in the field, and a 38 cm long sediment core was taken from the center of Jiren Lake using Hon-Kajak sediment corer(diameter is 90 mm) in 2014, and 0.5 cm divided in the field. Multi-proxies (i.e.,cladoceran, diatom, geochemical) from two lakes sediment cores over the past 200 years, 0~28.5 cm of Jiren Lake and 0 ~31 cm depth of Cuoqia Lake, were analysed, to reconstruct the environment change history of two Lakes,and to understand how physicochemical characteristics and catchment characteristics of lakes above and below treeline affect the composition of aquatic organisms (i. e.,cladocera and diatom) and their response to environmental change. Based on the ~(210)Pb/~(137)Cs dating, the chronology of two cores were established. The composition of cladocera are different in two oligotrophic lakes, littoral species(Alona spp., Pleuroxus spp. etc) and ubiquitous species Chydorus sphaericus are dominated in Jiren Lake,while the Cuoqia Lake was predominated by planktonic cladocera Daphnia longispina with rare littoral species. The diatom assemblages at Jiren Lake was predominated by small Fragilaria and Cyclotella. Aulacoseira spp. and benthic species were dominated at Cuoqia Lake. During the last 200 years, all cladocera and diatom composition showed obvious changes in Jiren Lake,while,there are subtle changes of diatom composition and only obsolete fluctuation between the dominate cladcera species D. longispina and predatory species Polyphemus pediculus at Cuoqia Lake. Our results indicates that,the composition of aquatic organisms (cladoceran and diatom) and their response to regional environmental change were mediated by lake altitude, lake physicochemical characteristics and catchment characteristics. Lower altitude and higher water temperature in Cuoqia Lake promote the growth of planktonic cladocera,besides, high DOM and DOC taken from the catchment not only provide more available food for cladocera, but also reduce the water transparent and UV radiation,and then benefit the survive of planktonic species in the open water zone. For the case of Jiren Lake, lower water temperature, shorter growth period and higher UV radiation intensity should restrained the growth of planktonic cladocera. Although there is no evidence of climate warming affect the composition changes of cladocera and diatom in two lakes, climate warming may contribute to the noticeable change of organisms in Jiren Lake indirectly. Higher altitude of Jiren Lake makes it more sensitive to climate change, and the degradation of increase temperature during the past 200 years should be higher than that in Cuoqia Lake, climate warming result in more glacial water inputs and reduced the pH of water body, ultimately changed the composition of cladocera and diatom. For the Cuoqia Lake, lower altitude and forest cover around the catchment buffer the increasing temperature, thus, no obvious change of aquatic organism in this lake.