Carnations are one of the most popular ornamental flowers in the world with varied flower colors that have long attracted breeders and consumers alike. The differences in carnation flower color are mainly the result of the accumulation of flavonoid compounds in the petals. Anthocyanins are a type of flavonoid compound that produce richer colors. The expression of anthocyanin biosynthetic genes is mainly regulated byMYBandbHLHtranscription factors. However, these TFs have not been comprehensively reported in popular carnation cultivars. Herein, 106MYBand 125bHLHgenes were identified in the carnation genome. Gene structure and protein motif analyses show that members of the same subgroup have similar exon/intron and motif organization. Phylogenetic analysis combining theMYBandbHLHTFs fromArabidopsis thalianaseparates the carnationDcaMYBs andDcabHLHsinto 20 subgroups each. Gene expression (RNAseq) and phylogenetic analysis shows thatDcaMYB13in subgroup S4 andDcabHLH125in subgroup IIIf have similar expression patterns to those ofDFR,ANS,andGT/AT, which regulate anthocyanin accumulation, in the coloring of carnations, and in red-flowered and white-flowered carnations,DcaMYB13andDcabHLH125are likely the key genes responsible for the formation of red petals in carnations. These results lay a foundation for the study ofMYBandbHLHTFs in carnations and provide valuable information for the functional verification of these genes in studies of tissue-specific regulation of anthocyanin biosynthesis.