In this study, the whole chloroplast genome sequence of Elaeagnus angustifolia Linn was assembled by sequencing total genome DNA with the second generation sequencing. Young leaves of E. angustifolia were collected from shoots of two wild individuals under hydroponic growth in greenhouse , and total DNA of the two individuals were extracted separately by CTAB method for two repeats of the chloroplast genome. The codon usage bias of proteincoding genes and its causes were analyzed in detail. The results of this study are of great significance for future chloroplast genetic engineering and molecular phylogenetic researches in E.angustifolia. The results show: (1) the full chloroplast genome sequence of E. angustifolia was a circular molecule of 150 546 bp in length with a typical quadripartite structure, including a pair of inverted repeats (IRA and IRB) of 25 494 bp that were separated by large and small single copy regions (LSC and SSC) of 81 113 bp and 18 445 bp, respectively. A total of 132 predicted genes, including 86 proteincoding genes, 39 tRNA genes and 8 rRNA genes, were identified. (2) The GC content of the third nucleotide in all proteincoding genes was 28.47%, which was significantly lower than that GC₂ and GC₁, indicating that the E. angustifolia chloroplast gene codon has a preference for the end of the A or T base, and eight optimal codons, UCU, CCU, UGU, GCU, CUU, GAU, UCA and UAA were determined. (3) We analyzed the codon bias of the chloroplast genomic protein coding sequence of E. angustifolia. Corresponding analysis of RSCU indicated that mutations, selection and other factors may all affect the codon usage pattern, and the sequence difference caused by natural selection is more significant than the mutation to codon usage bias. Effective Number of Codon plot (ENCplot) analysis and Parity rule 2 plot (PR2plot) analysis indicated that the bias of codons in the chloroplast genome of E. angustifolia was mainly influenced by selection, although mutation may also have played a role. (4) Cluster tree based on the Relative Synonymous Codon Usage (RSCU) values of chloroplast genes from seven species in Elaeagnaceae is basically consistent with phylogenetic tree based on chloroplast whole genome sequences, which illustrated that codon usage bias pattern in the chloroplast genomes of species in Elaeagnaceae was related to the phylogenetic relationship of these species.