Adaptive laboratory evolution of Yarrowia lipolytica PO1f in the benchmark ionic liquid (IL; 1-ethyl-3-methylimidazolium acetate) produced a superior IL-tolerant microorganism, strain YlCW001. Here, we report the genome sequences of PO1f and YlCW001 to study the robustness of Y. lipolytica and its potential use as a microbial platform for producing fuels and chemicals.