The genus Polygonatum boasts abundant germplasm resources and comprises numerous species. Among these, medicinal plants of this genus, which have a long history, have garnered attention of scholars. This study sequenced and analyzed the chloroplast genomes of six species of Polygonatum medicinal plants (P. zanlanscianense, P. kingianum, P. sibiricum, P. cyrtonema, P. filipes and P. odoratum, respectively) to explore their inter-specific relationships. The sequence length (154, 578–155, 807 bp) and genome structure were conserved among the six Polygonatum species, with a typical tetrad structure. The genomes contain 127–131 genes, containing 84–85 protein-coding genes, 37–38 transfer RNA genes, and 6–8 ribosomal RNA genes. The genomes contained 64–76 simple sequence repeats (SSRs) and 36–62 long repetitive sequences. Codon bias patterns tended to use codons ending in A/T. In thirty types of codons with RSCU > 1, 93.3% ended in A/T of the six species. Twenty-one highly variable plastid regions were identified in the chloroplast genomes of the six medicinal plants. In addition, phylogenetic analysis of these and other 53 Polygonatum chloroplast genomes showed that P. cyrtonema, P. odoratum and P. filipes were clustered on one large clade, whereas P. kingianum and P. zanlanscianense were clustered on other clades. P. sibiricum is a monophyletic group and our tree supports the classification of P. sibiricum as an independent clade. This study provides a novel basis for intragenus taxonomy and DNA barcoding molecular identification within the genus Polygonatum medicinal plants.