Abstract: This paper analyzed the codon usage in chloroplast genome of 2 Yulania species by Codon W, CUSP and R software. The results showed that the GC content of chloroplast genomes of 2 Yulania species was GC₁ > GC₂ > GC₃, which indicated the content of base A/U at codon 3 was high. The effective number of codons (ENC) of CDS sequences exceeding 45 were more than 80 base pair, and the average CAI value was 0.167, which indicated weak codon bias. The results of ENC−plot, PR2−plot and neutral plot analysis showed that the correlation among GC₁, GC₂ and GC₃ was not significant. And the usage frequency of the third base was T > A, G > C. It indicated that the formation of codon bias in chloroplast genome of 2 Yulania species was affected by natural selection and gene mutation cooperatively, and natural selection is the main affecting factor. According to the relative synonymous codon usage(RSCU)and ENC values, 30 optimal ciphers ending in A/U were selected. It was demonstrated that the codon 3 position in the chloroplast genome of 2 species of Yulania soulangeana and Yulania kobus has an A/U preference.