This study uses a choice experiment approach to examine whether different types of feedstocks as well as other attributes such as the cost of bioethanol, bioethanol blending ratio, and government support policies affect consumers’ biofuel preferences. We apply a standard conditional logit model, a mixed logit model (MLM), and individual coefficient estimation model (ICM) to estimate the parameters of the investigated attributes. The results show that people prefer domestic and non-food feedstock, along with tax exemption as a support policy. All the attributes show unobservable preference heterogeneity in the MLM and ICM. In particular, willingness to pay for attributes are higher in the genetically modified (GM) feedstock-unknown group than in the known one. We show the importance of using domestic and non-food feedstocks and managing GM feedstocks carefully to avoid consumer resistance when producing bioethanol in South Korea.