Large-scale production of biofuels and other highvalue products from microalgae focuses on strain selection with desired characteristics such as high lipid productivity and robustness. However, microalgae often suffer severe biomass losses due to contamination that comes in the form of herbivores, especially rotifers. In this study, we found that the total lipid content of 54 microalgal strains from Eastern China ranged from 12.6 to 59.9% of dry cell weight (dw), with an average of 35.4% dw. Lipid productivity of these microalgal strains varied from 0.04 to 0.14 g L −1 day, and 15 showed lipid production rates over 0.10 g L −1 day −1. The fatty acid profiles of 34 microalgal strains with lipid content over 40% dw were analyzed by gas chromatography. We found that the amount of C18:1 increased with increasing total lipid content, whereas C14:0 and C16:0 showed a negative correlation to the total amount of lipids. An experimental rotifer-microalgae predator-prey model was constructed, and the anti-rotifer robustness of these microalgal strains was evaluated. We found that Didymogenes sp. HN-4 can depress the growth of rotifers significantly. This study demonstrates the biodiversity of the native Chinese microalgae in lipid productivity and robustness, which lays the groundwork for mass algal culture.