Abstract: In this study, the complete chloroplast genome sequences of Pinus ponderosa P. Lawson & C. Lawson and Picea pungens Engelm. were determined using next-generation sequencing technology. The genome sizes of Pinus ponderosa and Picea pungens were 120 274 bp and 124 237 bp, respectively. The chloroplast genome of P. ponderosa contained 107 genes, including 70 protein-coding genes, four ribosomal RNA (rRNA) genes, and 33 transfer RNA (tRNA) genes. The chloroplast genome of P. pungens contained 111 genes, including 71 protein-coding genes, four rRNA genes, and 36 tRNA genes. In total, 18 and 32 simple sequence repeats were identified in the Pinus ponderosa and Picea pungens chloroplast genomes, respectively. Phylogenetic analysis using 73 common chloroplast genes from 19 Pinaceae and two outgroups divided Pinaceae into two groups: the first clade included Cedrus, Pseudolarix, Tsuga, Keteleeria, and Abies; the second clade included Pinus, Cathaya,Picea,Larix, and Pseudotsuga. Analysis of chloroplast genome structure identified several rearrangements between different genera of Pinaceae, mediated by a trnS-GCU small inverted repeat sequence.