4-Coumarate: coenzyme A ligase (4CL) catalyzes the conversion of hydroxycinnamates into corresponding CoA esters for biosynthesis of flavonoids and lignin. It has been widely studied in seed plants; however, it is poorly characterized in ferns. In this study, we identified 4CLs genes in ferns D. fragrans (L.) Schott (Df4CL gene) by rapid amplification of cDNA ends (RACE), and then investigated the expressions of the genes by real-time PCR, and determined total flavonoids and lignin contents. The results showed that four members of the 4CL genes were found from this species, which named Df4CL 1, 2, 3, and 4 genes. Their full-length cDNA was sequenced. Also, our analyses showed that the amino acid sequences derived from these cDNAs exhibited similar conserved regions (Box I and Box II), and substrate-binding regions compared to 4CLs isolated from seed plants.At the same time, the developmental and stress-induced gene expression patterns showed that the changes on the expression levels of Df4CL genes affected the levels of flavonoids and lignin. In conclusion, we identified 4CLs genes in ferns D. fragrans and analyzed the expressions of these genes, and finally explored the relationship between the expressions of 4CLs and syntheses of flavonoids and lignin.