The Indo-Pacific Convergence Region is the center of the origin in marine biodiversity and has extremely high biodiversity. With the dramatic changes in global climate and human activities intensify, ecosystems are gradually fragmenting. In this context, marine fish play important ecological functions in connecting fragmented ecosystems and protecting biodiversity. Exploring the genetic structure and connectivity of typical fish species in the Indo-Pacific Convergence Region Convergence Region will clarify the genetic diversity patterns and diffusion paths among different populations, thereby providing scientific support for the protection of biological diversity. In this study, 8 fish species (Acanthurus japonicus、Balistapus undulatus、Cephalopholis urodeta、Ctenochaetus striatus、Gnathodentex aureolineatus、Lutjanus kasmira、Melichthys vidua and Parupeneus multifasciatus) were collected from 5 representative areas in the Indo-Pacific Convergence Region (Zhongsha Islands, Nansha Islands, Xisha Islands, Hainan Island, and the Philippines), totaling 309 samples, 515 mitochondrial COI genes and 16 s sequences were obtained; To broaden the scope of the study, COI gene sequences from Taiwan Island in China and Indonesian were downloaded from GenBank, amounting to 86 sequences. Based on this, we analyzed the genetic diversity and genetic differentiation structure among different groups in the above seven study regions. The overall results show that 8 fish species have high levels of genetic diversity and low genetic differentiation, among which Parupeneus multifasciatus and Balistapus undulatus are the most obvious; Indonesia, Taiwan Island in China and South China Sea Island populations also have high genetic diversity. The study further developed the Species Distribution Models and the Least-cost paths model to explore the population connectivity. Based on this, distribution information for the eight fish species (collected from a total of 133,047 points) was used to predict suitable distribution areas under current climate using the MaxEnt algorithm, and the connectivity between different populations was calculated using the ArcGis 10.2 software SDMtoolbox v2.5. Population connectivity reveals that the east coast of the Philippines-Sulawesi is an important dispersal path for the above eight typical fish species in the Indo-Pacific Convergence Region. The South China Sea Islands (Nansha, Zhongsha and Xisha Islands) connect Taiwan Island in China, the Philippines and Indonesia, and serve as connecting hubs for species spread. In summary, the Philippines, Indonesia, Taiwan Island in China, and the South China Sea should become priority protected areas for maintaining genetic diversity and protecting connectivity. When protecting biodiversity, population connectivity and genetic diversity should be comprehensively considered, and different research results reflected at the macro and micro levels should be combined to achieve more effective biodiversity conservation.