Polygonatum odoratum (Mill.) Druce (Asparagaceae, Asparagales) is a widely cultivated medicinal herb in China. However, this useful herb is understudied despite being known as a medicinal resource with top grade medical and edible properties since long. In this study, P. odoratum and four cultivars were investigated. The variations in morphological characteristics and vegetative phases of each cultivars were observed. For genetic aspect, the plastid genome of P. odoratum varies in length from 154,569 bp to 155,491 bp, containing a large single-copy region of 83,486—84,459 bp, a small single-copy region of 18,292—18,471 bp, and two inverted repeats of 26,302—26,370 bp. A total of 131 genes were predicted, including 85 protein-coding, 38 tRNA, and eight rRNA genes. Genome comparisons revealed a slight variation in the sequence across the five accessions, but two highly variable regions (trnC-petN and rpl32-trnL) were detected when comparing the four different cultivars. For the RAD-seq markers, a total of 33.64 Gb of clean data, with an average value of 1.08 Gb per sample, were analyzed for presence of single nucleotide polymorphisms (SNPs). Well-resolved phylogenies of the P. odoratum cultivars are constructed; the non-monophyletic relationship in the plastome-based phylogenetic trees, yet monophyletic form in the RAD-based linkage map suggested possibility of hybrid cultivar for P. odoratum “Dazhu” (GDDZ), which was further supported by morphological observations. Quality assessment based on the standards of the Chinese Pharmacopoeia on Polygonati Odorati Rhizoma (POR) on the four cultivars used in this study recorded that PORs from P. odoratum ‘Zhongzhu’ (GDZZ) met the minimum criteria for the acceptance as raw material for medicinal drug production. This study has provided insights on the morphological variations, genetic background, and medicinal qualities of P. odoratum cultivars that could be explored for future genetic improvement as well as breeding programs of P. odoratum for POR production.