Abstract  [Aim]  The tomato leaf miner, Tuta absoluta (Meyrick), is a major pest of tomato crops, causing significant economic  losses since invading China. The genetic structure of the tomato leaf miner population in China was analyzed to trace its genetic differentiation process and analyze its genetic relationship with other geographic populations around the world. [Methods]  The study used the mitochondrial COⅠ gene as a molecular marker, and analyzed the COⅠ gene similarity, genetic variation, genetic diversity, and biomolecular variation composition. We then constructed a global phylogenetic tree. [Results]  Our results demonstrate that mutant individuals have developed in the Gansu and Ningxia regions of China. Two mutant haplotypes were found in Gansu, and one mutant haplotype was found in Ningxia. A total of 28 polymorphic loci and 18 haplotypes were identified in the geographic populations of tomato leaf miners globally. Senegal had the most haplotypes with 10, followed by Kenya. In China, two parsimony-informative loci for the conversion mutation were present with a total of three haplotypes. Additionally, a Tajima's test indicated a post-invasion population expansion of the tomato leaf miner had occurred. Overall, the genetic diversity of the tomato leaf miner was relatively high in Africa, followed by South America and Asia. ANOVA analysis revealed that within population factors explained 97.99% of the population variation. Phylogenetic analysis showed that the Kenyan variant KP324753.1 was an independent taxon. The tomato leaf miner populations China: GSLZ in Lanzhou, Gansu, and China: NX in Ningxia, were the same taxon as the Kenyan variant KU565664.1. Furthermore, the genetic distance was similar to that of the China: GSZY Zhangye variant in Gansu Province, even though it was identified as a different taxon. [Conclusion]  Globally, the tomato leaf miner moth exhibited low genetic diversity indices, and highly homogenous population genetics. The population of tomato leaf miners in China have undergone molecular differentiation, and the population may be currently expanding following the invasion bottleneck.