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Pinus pumila is a rare and endangered conifer plant in the family Pinaceae. Here, we determined the complete chloroplast (cp) genome sequence of P. pumila. The cpDNA was 117,398 bp in length, containing a pair of 475 bp inverted repeat regions (IR), which was divided into large single copy region (LSC) and small single copy region (SSC) with 64,606 and 51,842 bp in length, respectively. The GC content in cpDNA, LSC region, SSC region and IR region were 38.8%, 38.0%, 39.8% and 37.9%, respectively. The cpDNA contained 114 genes, including 74 protein-coding genes (CDS), 36 transfer RNA genes (tRNA) and 4 ribosomal RNA genes (rRNA). A phylogenetic analysis revealed that P. pumila is more closely related with congeneric P. fenzeliana var. dabeshanensis and P. sibirica.