Caffeoyl coenzyme A-O-methyltransferase (CCoAOMT) has a critical function in the lignin biosynthesis pathway. However, its role in pomegranate is not clear. In this research, we identified 11 members of the CCoAOMT gene family based on pomegranate genome-wide data. The 11 CCoAOMT genes were distributed non-uniformly on chromosomes 2, 3 and 4 of pomegranate. Phylogenetic analysis showed that pomegranate CCoAOMT9 and Camellia sinensis CCoAOMT genes clustered into one branch. Promoter cis-acting progenitor analysis revealed a role for the pomegranate CCoAOMT gene in the ABA/MeJA response. The expression of CCoAOMT8, CCoAOMT9 and CCoAOMT10 was higher in hard-seeded cultivars (‘Hongyushizi’ and ‘Baiyushizi’) than in soft-seeded cultivar (Tunisia) as detected and analyzed by q-PCR. The results suggested that CCoAOMT8, CCoAOMT9, and CCoAOMT10 might be related to lignin biosynthesis. The findings of this work provided a basis for further investigation of the role of the pomegranate CCoAOMT gene in lignin biosynthesis.