Chimonocalamus is a medium sized genus with distinguished morphological characteristics at the generic level. However, species identification in this genus can be confused due to similar morphological features and overlapped geographical distribution. To clarify the delimitation and confirm the identities of Chimonocalamus species in China, plastomes and nrDNAs 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 five datasets. Meanwhile, Skmer method was also exploited. The results indicated that Skmer analyses had the highest discriminatory power with nine species identified (69.23%). The plastomes showed much higher discriminatory success rate than the combination of three standard plastid DNA barcodes which performed worst among the five datasets. According to the tree-based analysis, the C. fimbriatus complex was designated. This complex bears few morphological differences and the species delimitation needs to be further studied at the population level. Nevertheless, the three potentially new species of Chimonocalamus were confirmed by the plastome and nrDNA datasets, and Skmer analysis, together with morphological difference. Herein, we described and illustrated them as new to science, i.e., C. hekouensis Y. X. Zhang, Gui L. Zhang & D.Z. Li, C. hsuehiorum D.Z. Li & Y.X. Zhang, and C. shuangjiangensis D.Z. Li & Y.X. Zhang. Taken together, plastomes and nrDNAs 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.