We investigated historical changes in temperature and phytoplankton in Fuxian Lake (FX) and Dianchi Lake(DC), two plateau lakes in Southwest China. We detected sterols and alkyl diols as algal biomarkers (dinoflagellates, diatoms, eustigmatophytes, cyanobacteria, and chlorophyta) in the sediment cores by using GC-MS. We characterized sedimentary organic matter (SOM) via Rock-Eval analysis to obtain TOC, S2, the hydrogen index (HI), and refractory carbon (RC), and measured nutrients such as total phosphorus (TP) and total nitrogen (TN) in the sediment cores. The results showed that the sedimentation rates measured by ²¹⁰Pb dating ranged from 0.02 to 0.30 g cm^-2 yr^-1 and 0.07 g cm^-2 yr^-1 in FX and DC, respectively. In the past 100 years, total phytoplankton biomarker concentrations ranged from 2.25 µg g^-1 to 59.1 µg g^-1 and from 2.20 µg g^-1 to 76.4 µg g^-1 in FX and DC respectively. Primary productivity derived from the S2 and HI parameters showed an increasing trend in FX, while it showed a trend of first increasing and then decreasing in DC. Cyanobacteria and chlorophyta were the two dominant phylum in the two lakes. Algal growth was controlled primarily by temperature and nutrient availability. Principal component analysis (PCA) and multiple linear regression analysis showed that the major factors controlling the historical change in phytoplankton growth were TN and temperature in FX and DC.