The ubiquitin/26S proteasome pathway plays an important role in response to abiotic stress in plants. E2 (ubiquitin-binding enzyme, UBC), which is an ubiquitin-binding enzyme involved in protein ubiquitination, participates in the protein degradation pathway in a complex with E1 and E3. In this study, we identified 54 soybean UBC genes using hidden Markov model, and the family members were divided into 8 subfamilies (A-K) according to the phylogenetic tree analysis. Protein conserved domain analysis indicated that GmUBC family proteins contain conserved domains 1, 2 and 3, which belong to the conserved domain of ubiquitin-binding enzymes. Tissue expression analysis indicated that the transcripts of GmUBC family genes were detected in soybean roots, stems, leaves, flowers and other tissues. Transcriptome data indicated that a diversifying expressional pattern was observed for 20 GmUBC genes under drought, salt or cold stress treatments. Analysis for cis-elements in the promoter suggests that some of GmUBC genes may be involved in hormonal signaling. Furthermore, qRT-PCR analysis showed that GmUBC46 was inducible under drought, salt and cold stresses. Expressing the GmUBC46 gene in yeast showed a decreased tolerance in responses to drought and salt stress treatments. In summary, this study revealed the basic characteristics of UBC gene family in soybean and the preliminary functional insight of GmUBC46, and gain of datasets might provide considerable basis and reference value for future research.