The relationship between the co-occurrence of cryptic zooplankton species and environmental variables was studied in a lake in China. Lake Jinghu was sampled for zooplankton and water chemistry at 3 or 4-day intervals over a year, and samples of the rotifer Brachionus calyciflorus were obtained at 8-day intervals and clonally cultured in the laboratory. We found that B. calyciflorus occurred in winter and spring, and was a species complex composed of cryptic species BcI and BcII based on mtDNA COI sequence divergence and the GMYC model analyses. Both cryptic species cohabited in Lake Jinghu when they were present. The densities of BcI and BcII were not correlated, indicating that there might be no strong competition between them. Based on principal component analysis (PCA) and generalized linear models (GLM), only BcII density was impacted by chlorophyll a (Chl a) concentration (of the lake water filtered through a 25 μm net) alone with a time lag, and the interaction of temperature and Chl a concentration without a time lag. Our results suggest that a distinct response to Chl a reduces the intensity of competition between cryptic B. calyciflorus species and promotes their coexistence in Lake Jinghu over time.