Abstract: Chimonocalamus is distinguished by pachymorph rhizome, lower culm nodes with a ring of root thorns, and semelauctant inflorescence. However, species identification in this genus can be confused due to similar morphological features and overlapped geographical distribution. To confirm the identities of Chimonocalamus species in China, plastome and nuclear ribosomal (nrDNA) of 49 accessions of 10 known species and three putative new species were newly retrieved by genome skimming. Distance-based and tree-based methods were conducted to analyze the species discrimination rate of six datasets. The Skmer method was also applied. The results indicated that Skmer analyses had the highest discriminatory power with nine species identified (69.23%). The plastome showed much higher discriminatory success rate than the combination of three standard plastid DNA barcodes, which performed worst among the six datasets. The three potentially new species of Chimonocalamus were confirmed by the plastome and nrDNA datasets, and Skmer analysis, together with morphological differences. Herein, we describe and illustrate the three species as new to science, that is, Chimonocalamus hekouensis Y. X. Zhang, Gui L. Zhang & D. Z. Li, Chimonocalamus hsuehiorum D. Z. Li & Y. X. Zhang, and Chimonocalamus shuangjiangensis D. Z. Li & Y. X. Zhang. Moreover, the Chimonocalamus fimbriatus complex was designated, calling for further investigation. Taken together, plastome and nrDNA could serve as effective super-barcodes for species discrimination of Chimonocalamus, playing important roles in recognition of cryptic new species, and Skmer analysis can be adopted in molecular identification. Our study provides an empirical case for molecular discrimination of bamboos and can be meaningful for other plant groups.

Key words: Chimonocalamus, cryptic species, genome skimming, Skmer, super‐barcode