The fungus Raffaelea quercus-mongolicae is the causal agent of Korean oak wilt, a disease associated with mass mortality of oak trees (e.g., Quercus spp.). The fungus is vectored and dispersed by the ambrosia beetle, Platypus koryoensis Here, we present the 27.0-Mb draft genome sequence of R. quercus-mongolicae strain KACC44405.