Berberidis Radix (Sankezhen), a typical multi-origin Chinese medicinal material, originates from the dried roots of the Berberis genus plants and is used to treat a range of ailments. These species have similar morphology potentially leading to misidentification that can impact the medicine's efficacy. Therefore, it is imperative to develop suitable molecular markers to identify medicinal species. Furthermore, discrepancies exist in the taxonomy of the Berberis genus. In the current study, we de novo assembled the chloroplast genomes of six Berberis species (Berberis julianae, Berberis tsienii, Berberis pruinosa, Berberis thunbergii, Berberis poiretii, and Berberis wilsoniae) that commonly constitute Berberidis Radix and compared them with previously reported genomes. Our comparative analysis revealed similarities in genome structure, relative synonymous codon usage, amino acid frequency, repeats, and substitutions. Higher synonymous substitutions, indicative of predominant purifying selection on protein-coding genes, were observed compared to non-synonymous substitutions. However, positive selection was identified for six genes across 29 Berberis species—accD, matK, ndhD, rbcL, ycf1 and ycf2—highlighting their potential roles in adaptive responses to specific environmental conditions within the genus. Inverted repeats expansion and contraction affected the rate of mutations and is associated with the phylogenetic classification of Berberis. Our phylogenetic analysis supported the division of the Berberis complex into four genera, which corroborates the findings of previous studies involving extensive sampling. We identified the ndhD-ccsA region as the most polymorphic region and applied this region to Chinese patent medicines containing Berberidis Radix through metabarcoding. Metabarcoding analysis confirmed that five Berberis species commonly constitute Berberidis Radix in Chinese patent medicines. In conclusion, this study provides insight into the molecular evolution of the chloroplast genome and the phylogeny of the Berberis genus. In addition, through metabarcoding, provides insight into the species composition of Berberidis Radix in Chinese patent medicines.