In Volvariella volvacea, a species of edible mushroom, cryogenic autolysis is a typical part of abnormal metabolism. Previous functional annotation cluster analyses of cold-induced gene expression profiles have shown that the ubiquitin-conjugating enzyme E2 (UBE2) and the cyclin-like F-box domain (FBDC) form the functional clusters. Among them, a specific FBDC gene has been found to be in response to cold stress and correlated with the cryogenic autolysis of V. volvacea. In this study, analysis of gene expression profiling showed that only one type of UBE2 in V. volvacea (UBEV2) was significantly up-regulated. Further quantitative real-time PCR analysis confirmed that the expression of UBEV2 was significantly up-regulated (P < 0.05) after cold-treatment lasting 4, 6, and 8 h. Western-bolt analyses confirmed that the protein expression of UBEV2 was in response to cold stress. This provided evidence that UBEV2 was a cold stress-responsive gene and closely correlated with cryogenic autolysis. The specific distribution of UBEV2 in recently diverged herb decay fungi indicated that UBEV2 was not evolutionarily correlated with early diverging fungi. Phylogenetic analysis indicated that UBEV2 was generated by horizontal gene transfer (HGT) from the ancestry of Selaginella moellendorffii UBE2. Further relative time estimation and detection of natural selection showed that there has been recent positive selection after HGT in UBEV2. Molecular modeling and logo analysis showed that the cysteine-cysteine motif is the characteristic of the UBEV2 family. These observations indicate that UBEV2 and FBDV1 are the newly discovered cold stress-responsive genes correlated with the cryogenic autolysis of V. volvacea.