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The whole chloroplast genome sequence of Populus afghanica is characterized in this study. The size of cp genome of P. afghanica is 155,975 bp, containing a large single-copy region (LSC) of 84,223 bp, a small single-copy region (SSC) of 16,504 bp, and a pair of identical inverted repeat regions (IRa, b) of 27,624 bp. The overall GC content of the chloroplast genome is 36.8%. One hundred twenty-eight genes were annotated, including 81 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The maximum-likelihood phylogenetic analysis with the reported chloroplast genomes showed that P. afghanica is sister to Populus lasiocarpa Oliv., implied a hybridization orign.