Abstract: The characteristic of codon usage bias(CUB), codon base composition, relative synonymous codon usage(RSCU) were analyzing using software CodonW 1.4.2 and online program CUSP with effective number of codons(ENC) of 17369 coding sequences(CDS) from Gerbera jamesonii transcriptome data, and clarifying the main influencing factors of CUB by neutrality plot, ENC−plot and PR2−plot analysis. The results revealed that the CUB value is low in the whole CDS ofG. jamesonii and the major factor of CUB in the whole CDS was mutation. A total of 13 codons, including UUG, UUU, UAU, AUU, UGU, GUU, AGA, GGU, UCU, UCA, CCA, ACC and GCU, were identified for the optimal codons in G. jamesonii, and the optimal codons generally end with A/U at the third position. The present study can provide beneficial information to further define the evolution character of G. jamesonii codons, and take some basis for the selection of the optimal codons in genetic transformation ofG. jamesonii.