Bidens pilosa is an annual invasive and Cd-hyperaccumulator herb. The complete chloroplast genome sequence of the B. pilosa is 150,542 bp in length, which is composed of a large single-copy region of 83,542 bp, a small single-copy region of 17,624 bp and a pair of inverted repeat regions of 24,688 bp. It encodes a set of 114 genes, consisting of 80 protein coding, 30 tRNA and 4 rRNA genes. Among all of these genes, 2 genes possess double introns, and 16 genes have a single intron. Phylogenetic analysis showed that B. pilosa clustered together with Marshallia obovata.