Alfalfa (Medicago sativa) is a forage legume with high feed quality widely cultivated all over the world. It contains lignins that play an important role in stress resistance of alfalfa. However, lignin seriously affects the nutritional value of alfalfa because it is difficult for livestock to digest. Therefore, it is necessary to breed alfalfa varieties with low lignin content. Caffeoyl CoA O-methyltransferase (CCoAOMT) is a key enzyme in the lignin synthesis pathway. In this study, the members of CCoAOMT gene family in the alfalfa genome were identified by bioinformatic methods, and the gene structure, chromosome location, phylogeny and gene expression were analysed. It was found that there were 44 MsCCoAOMT genes in the alfalfa genome. These genes were distributed on 16 chromosomes with tandem duplication, among which 36 (82%) MsCCoAOMT genes contained 5 exons. A phylogenetic tree was constructed and showed that MsCCoAOMT family genes can be classified into 5 groups. In addition, ten conserved motifs were found by predicting the motif of MsCCoAOMT protein with MEME software. qRT-PCR results indicated that most of MsCCoAOMT genes were tissue-specific in their expression. Our results provide reference information for the genetic improvement of alfalfa and development of lines with low lignin content.