To broaden our knowledge of flower development, two floral homeotic genes, LbAG and LbSEP3, were isolated from the flower of Lycium barbarum L. The open reading frame length of LbAG and LbSEP3 were 1090 and 992 bp encoding 249 and 242 amino acids, respectively. Sequence alignment and phylogenetic analysis indicated that LbAG belonged to C-type MADS-box gene and that LbSEP3 was E-type MADS-box gene. Compared with other floral homeotic proteins, LbAG held the conserved AG motif I, II and LbSEP3 conserved SEP3 motif I, II. Expression profile showed that LbAG transcripts were abundant in inner two whorls and fruit but not in root, leaf, sepal, and petal, and that LbSEP3 constitutively expressed in root, leaf, fruit, and all the four floral whorls.