Hygrophila polysperma is a type of amphibious plant that originates from Acanthaceae. Here, we report its first complete chloroplast (cp) genome. The complete cp genome is 146,675 bp in length with 38.3% of GC content. There are 130 genes including 86 protein coding genes, 36 tRNA genes, and 8 rRNA genes in this genome. Simple short sequence (SSR) analysis found 30 SSRs, 24 of which are located in a large single-copy region. Nucleotide diversity identified six most divergent sequences (trns-GCU, psaA-pafI, psaI-pafII, ycf2, rpl32, and ycf1) among 3 close-related species, H. polysperma, H. ringens, and Asteracantha longifolia. A phylogenetic tree among H. polysperma and another 30 related species was constructed based on the common coding sequence of the cp genome and showed that H. polysperma is most closely related to H. ringens (both belong to subtribe Hygrophilinae) and, together, they form a clade that is sister to A. longifolia. This study provides a basis for systemic and evolution studies as well as the development of molecular markers for species identification and genetic breeding.