AP1 (APETALA 1) gene might be associated with regulation of floral organ development in Paeonia lactiflora. To understand codon bias features of AP1 gene and for further selecting appropriate expression systems, AP1 gene was analyzed via online programs of Codon W, CHIPS and CUSP on the basis of previous molecular cloning of P. lactiflora (the accession number: KC354376), it was also compared among AP1 genes and other 12 plant species and genomes in model organisms. The results showed that most of the AP1 genes had bias toward the synonymous codons with A and T at the third codon position. There were 29 biased codons with the RSCU value larger than 1, and among of them, the stronger biased codons were CCA, AGG, TCA and GTT with the RSCU value larger than 2. By comparison the bias of AP1 genes with that of 12 plant species, it also found that gene expression levels in Mangifera indica and Pyrus pyrifolia were higher, while they showed common in Paeonia lactiflora and Paeonia suffruticosa wtih the bias toward the synonymous codons with A and T at the third codon position, which was related to specific functions of the gene. The results from the clustering analysis showed that Paeonia lactiflora and Paeonia suffruticosa belonged to Paeoniaceae, while Pyrus pyrifolia and Prunus persica belonged to another. The differences in codon usage frequency between AP1 gene and yeast genome were less than those of other two kinds of model organisms’ genomes. Therefore, the eukaryotic yeast expression systems might be more suitable for the expression of AP1 gene. This study could provide certain theoretical base for selecting the appropriate receptor plant and expression systems in genetic improvement, as well as improving the expression level of AP1 gene.