Background: Genotyping-by-sequencing (GBS), as one of the next generation sequences, has been applied to large scale genotyping in plants, which is poor in morphological differentiation and low in genetic divergence among different species. Curcuma is a significantly medicinal and edible genus. Improvement efforts of phylogenetic relationships and disentangling species are still a challenge due to poor morphology and lack in a reference genome. Result: A high-throughput genomic sequence data which was obtained through GBS protocols was used to investigate the relationships among 8 species with 60 total samples of Curcuma. Through the use of the ipyrad software, 437,061 loci and 997,988 filtered SNPs without reliance upon a reference genome were produced. After quality control (QC) of the filtered SNPs, 1,295 high-quality SNPs were used to clarify the phylogenetic relationships among Curcuma species. Based on these data, a supermatrix approach was used to speculate the phylogeny, and the phylogenetic trees and the relationships were inferred . Conclusions: Varying degrees of support can be explained, as well as the diversification events for Chinese Curcuma. The diversification events showed that the third intense uplift of Qinghai–Tibet Plateau (QTP) and formation of the Hengduan Mountains may speed up Curcuma interspecific divergence in China. The PCA suggested the same topology of the phylogenetic tree. The genetic structure analysis revealed that extensive hybridization may exist in Chinese Curcuma. Additionally, the GBS will be a promising approach for the phylogenetic and systematic study in the future.