Thrips are tiny insects that are difficult to identify morphologically, but molecular marker has become a wellestablished method of identification. To explore the phylogenetic relationships among species in the genus Trichromothrips of the large family Thripidae, 3 genes: a mitochondrial gene, COI (cytochrome c oxidase subunit I), and two nuclear genes, ITS2 (internal transcribed spacer 2) and 28S (28S ribosomal DNA), were used to construct single-gene and multi-locus phylogenetic trees of 24 samples in seven species. The single-gene BI (Bayesian inference) trees have different results, revealing the possible instability of constructing phylogenetic trees from single genes in this genus. Therefore, multi-locus phylogenetic trees were constructed using the BI and ML (Maximum likelihood) methods, and the results differ from all single-gene trees as well. Furthermore, this study proposed one potential new species (T. sp. “Jinping, Yunnan”) and two newly recorded species (T. alis and T. formosus) in China. The results of this study improved our understanding of the evolutionary relationships among species within the genus Trichromothrips.