Saccharomycopsis fibuligera MBY1320 was isolated from Nuruk, a traditional Korean starter for makgeolli (rice wine) production. This isolate has previously been reported to exhibit thermotolerance and starch-degrading activities. In this data description, we present the draft genome sequence of S. fibuligera MBY1320. The genome contained 19,138,941 bp in 16 contigs, and the internal transcribed spacer region of S. fibuligera MBY1320 rRNA gene showed the highest similarity with that of S. fibuligera NRRL Y-2388. The BioProject sequence has been deposited at DDBJ/EMBL/GenBank and Mendeley database. The GenBank accession numbers are PRJNA598085 for the BioProject data, SAMN13698230 for the BioSample data, and GCA_012062855 for the GenBank data.