Two cDNA clones designated GhUBC1 and GhUBC2 encoding ubiquitin-conjugating enzymes (E2s) have been isolated from a cotton (Gossypium hirsutum L. Cultivar St213) root cDNA library. They encode Class I E2s of 148 amino acids (aa) with calculated molecular masses of 16 kDa. The encoded GhUBC1 and GhUBC2 proteins are 98% identical to each other, and 78-96% identical to Arabidopsis thaliana AtUBC8-10, Oryza sativa OsUBC, and Saccharomyces cerevisiae ScUBC4-5 at the aa sequence level. The homology to ScUBC4-5 suggests that GhUBC proteins are probably involved in the selective degradation of abnormal and short-lived proteins. Northern blot analysis revealed that GhUBC1 and GhUBC2 are expressed in roots, flowers, and fibers, with the highest level in roots. Genomic Southern analyses indicated that there are two members of the E2 subfamily in the cotton genome. The GhUBC1 and GhUBC2 genes were amplified by PCR from cotton genomic DNA and sequenced by the dideoxy chain termination method. Genomic origin analysis indicated that GhUBC2 was present in the D subgenome of Gossypium hirsutum.