To identify the members of the UDP-glycosyltransferase(UGT) gene family in the genome of Citrus medica C-05 and to explore the roles of UGT genes in disease resistance and stress tolerance, the members of the UGT gene family were characterized and bioinformatic analysis was conducted based on the genomic information of Citrus medica C-05, and their expression profiles in response to infection by Xanthomonas citri subsp. citri(Xcc) and other stresses were analyzed. The results showed that a total of 56 UGT gene family members were identified in the Citrus medica genome, which were inferred to be widely involved in plant growth and development, hormone responses, and stress tolerance. The CmUGT proteins were further classified into 11 subgroups. Based on transcriptome data from leaves of resistant Citrus medica C-05 and susceptible Citrus sinensis, as well as RT-qPCR validation, three genes including CmUGT20, CmUGT43 and CmUGT44 were significantly upregulated upon Xcc infection, and their expression levels in Citrus medica C-05 were markedly higher than those in Citrus sinensis. The expression of Citrus sinensis UGT43 gene was found to be upregulated under waterlogging stress and co-infection with Candidatus Liberibacter asiaticus and citrus tristeza virus. It was revealed that UGT43 might play an important role in regulating citrus stress tolerance and disease resistance.