Genus Polygonatum Mill. (Asparagaceae) comprises 70 taxa and most are particularly well appreciated in East Asia for the various commercial uses. Despite the increased recognition for its commercial value, the taxonomy and phylogenetic relationships among congeners remain elusive. Polygonatum odoratum complex is a great example of the taxonomic conflicts in the genus. The complex consists of 7 taxa with high morphological diversity (P. odoratum var. odoratum, P. odoratum var. pluriflorum, P. thunbergii, P. robustum, P.grandicaule, P. lasianthum, P. infundiflorum), however species boundaries and the taxonomic identities of the taxa are ambiguous. In the present study, we aim to delimit species boundaries and understand the phylogenetic relationships among P. odoratum complex. First, we carefully examined the key morphological characters of P. odoratum complex from ~2,000 herbarium specimens. Genome-scale phylogeny of P. odoratum complex taxa was inferred by targeted gene capture with publicly available 353-angiosperm single copy gene probe sets. We also reconstruct chloroplast phylogeny using off-target sequences obtained from target capture sequencing. Maximum likelihood algorithm with 1000 bootstrap replicates and multi-species coalescent model were used for tree building and node support evaluation respectively in RAxML v8.2.12 and Astral v5.7.1. To investigate admixture proportion among the taxa, we performed ADMIXTURE analysis with 813 SNPs identified from the target capture data. 32 morphological characters measured failed to discriminate most taxa in the complex except for Polygonatum lasianthum from the rest. Overall, phylogenies of nuclear and chloroplast genes showed discrepancy on several clades. In the nuclear gene tree, we found three major clades representing three species previously recognized as Polygonatum odoratum, Polygonatum lasianthum and P. infundiflorum. Our result suggests that 7 taxa in the P. odoratum complex should be re-arranged to three species P. odoratum, P. infundiflorum, and P. lasianthum although additional samples collected outside of East Asia may improve the results.