Abstract: CodonW, CHIPS and CUPS programs were used to analyze the codon bias of psbA gene from 60 species of Liliaceous plants. As a result, 26 codons were preferable, of which 12 codons were very strong; whereas 10 codons were seldom used and 13 codons did not appear. The average ENc value of 37.84 indicated that the overall preference was weak. The average values of GC and GC3s were 42.5% and 48.0%, respectively, indicating that A and U were frequently used in both the total composition and the 3rd codon position. The CAI value of 0.218 indicated that the codon expression level was low. ENc-plot analysis showed that codon preference was mainly due to selection．The cluster analysis showed that the clustering based on the CDS sequence was better than that based on the RSCU value in the genetic relationship among all the Liliaceae plants, and it was more suitable as a reference for phylogenetic analysis of the family of the Liliaceae.

Key words: codon bias, cluster analysis, Liliaceae, psbA gene