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Taxus  (yew) is both the most species-rich and taxonomically difficult genus in Taxaceae. To date, no study has elucidated the complexities of the plastid genome (plastome) or examined the possibility of whole plastomes as super-barcodes across yew species worldwide. In this study, we sequenced plastomes from two to three individuals for each of the 16 recognized yew species (including three potential cryptics) and  Pseudotaxus chienii . Our comparative analyses uncovered several gene loss events that independently occurred in yews, resulting in a lower plastid gene number than other Taxaceous genera. In  Pseudotaxus  and  Taxus , we found two isomeric arrangements that differ by the orientation of a 35 kb fragment flanked by “ trnQ -IRs”. These two arrangements exist in different ratios within each sampled individual, and intraspecific shifts in major isomeric arrangements are first reported here in  Taxus . Moreover, we demonstrate that entire plastomes can be used to successfully discriminate all  Taxus  species with 100% support, suggesting that they are useful as super-barcodes for species identification. We also propose that  accD  and  rrn16-rrn23  are promising special barcodes to discriminate yew species. Our newly developed  Taxus  plastomic sequences provide a resource for super-barcodes and conservation genetics of several endangered yews and serve as comprehensive data to improve models of plastome complexity in Taxaceae as a whole and authenticate  Taxus  species.

Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide