SambucusL. is found in the family Viburnaceae (syn. Adoxaceae) and encompasses approximately 29 accepted species. The complex morphology of these species has caused continued confusion concerning their nomenclature, classification, and identification. Despite previous attempts to resolve taxonomic complexities in theSambucusgenus, there are still unclear phylogenetic relationships among several species. In this study, the newly obtained plastome ofSambucus williamsiiHance. as well as the populations ofSambucus canadensisL.,Sambucus javanicaBlume, andSambucus adnataWall. ex DC were sequenced, and their sizes, structural similarity, gene order, gene number, and guanine–cytosine (GC) contents were analyzed. The phylogenetic analyses were conducted using the whole chloroplast genomes and protein-coding genes (PCGs). The findings revealed that the chloroplast genomes ofSambucusspecies exhibited typical quadripartite double-stranded DNA molecules. Their lengths ranged from 158,012 base pairs (bp) (S. javanica) to 158,716 bp (S. canadensisL). Each genome comprised a pair of inverted repeats (IRs), which separated the large single-copy (LSC) and small single-copy (SSC) regions. In addition, the plastomes contained 132 genes, encompassing 87 protein-coding, 37 tRNA, and four rRNA genes. In the simple sequence repeat (SSR) analysis, A/T mononucleotides had the highest proportion, with the most repetitive sequences observed inS. williamsii. The comparative genome analyses showed high similarities in structure, order, and gene contents. The hypervariable regions in the studied chloroplast genomes weretrnT-GGU,trnF-GAA,psaJ,trnL-UAG,ndhF, andndhE, which may be used as candidate barcodes for species discrimination inSambucusgenus. Phylogenetic analyses supported the monophyly ofSambucusand revealed the separation ofS. javanicaandS. adnatapopulations.Sambucus chinensisLindl. was nested withinS. javanicain the same clade, collaborating their conspecific treatment. These outcomes indicate that the chloroplast genome ofSambucusplants is a valuable genetic resource for resolving taxonomic discrepancies at the lower taxonomic levels and can be applied in molecular evolutionary studies.