TheDalbergiaplants are widely distributed across more than 130 tropical and subtropical countries and have significant economic and medicinal value. Codon usage bias (CUB) is a critical feature for studying gene function and evolution, which can provide a better understanding of biological gene regulation. In this study, we comprehensively analyzed the CUB patterns of the nuclear genome, chloroplast genome, and gene expression, as well as systematic evolution ofDalbergiaspecies. Our results showed that the synonymous and optimal codons in the coding regions of both nuclear and chloroplast genome ofDalbergiapreferred ending with A/U at the third codon base. Natural selection was the primary factor affecting the CUB features. Furthermore, in highly expressed genes ofDalbergia odorifera, we found that genes with stronger CUB exhibited higher expression levels, and these highly expressed genes tended to favor the use of G/C-ending codons. In addition, the branching patterns of the protein-coding sequences and the chloroplast genome sequences were very similar in the systematic tree, and different with the cluster from the CUB of the chloroplast genome. This study highlights the CUB patterns and features ofDalbergiaspecies in different genomes, explores the correlation between CUB preferences and gene expression, and further investigates the systematic evolution ofDalbergia, providing new insights into codon biology and the evolution ofDalbergiaplants.