ISG15 was the first ubiquitin-like modifier to be identified. However, the function of ISG15 modification has been an enigma for many years. At present, no data are available about the function of ISGylation for any target. In this paper, we report the identification of Ubc13, which forms a unique ubiquitin-conjugating enzyme (Ubc) complex with ubiquitin enzyme variant Mms2 and generates atypical Lys63-linked ubiquitin conjugates, as one of the targets of ISG15 modification. Furthermore, we identify Lys92 as the only ISG15 modification site in Ubc13, which is the first report about the ISG15 modification site. Using the "covalent affinity" purification assay, we found that unmodified Ubc13 can bind to the ubiquitin-agarose, whereas ISGylated Ubc13 cannot. This result indicates that ISGylation of Ubc13 disrupts its ability to form thioester bond with ubiquitin.