Pseudostellaria palibiniana which belongs to subseries Verticilatae is one of the species in Pseudostellaria palibiniana species complex (PPSC). To uncover intraspecies variation of P. palibiniana, we presented its second complete chloroplast genome which is 149,639 bp long and has four subregions: 81,286 bp of large single copy and 16,977 bp of small single copy regions are separated by 25,688 bp of inverted repeat regions including 126 genes (81 protein-coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content is 36.5\% and those in the LSC, SSC, and IR regions are 34.3\%, 29.4\%, and 42.4\%, respectively. Eighty-four single nucleotide polymorphisms and 125 insertions and deletions are identified between two individuals of P. palibiniana. Phylogenetic tree presents that P. palibiniana isolated from the same place of Pseudostellaria longipedicellata is clustered with another P. palibiniana, showing that PPSC can be solved using complete chloroplast genomes.