Abstract
The family Acestrorhamphidae, comprising fish species with high nutritional and ornamental value, continues to face significant controversies regarding their systematic classification and evolutionary relationships. Due to notable convergent evolution and intraspecific variation in morphological characteristics, traditional morphological methods struggle to achieve reliable taxonomic delineation. In this study, high-throughput sequencing technology was employed to sequence and assemble the mitochondrial genomes of two species, Moenkhausia rubra and Moenkhausia nigromarginata, with lengths of 16,439 and 16,461 bp, respectively. Both genomes exhibit the typical mitochondrial gene structure of vertebrates, along with a distinct AT base bias and an anti-G bias. A phylogenetic tree constructed based on the mitochondrial genomes of 41 closely related species revealed that the genus Moenkhausia is monophyletic, with M. nigromarginata and M. rubra clustering together, indicating a close genetic relationship between the two species. On the other hand, the genus Hyphessobrycon was confirmed to be a paraphyletic group, with some of its species clustering together with species from the genera Gymnocorymbus, Hemigrammus, and Pristella. Additionally, the phylogenetic analysis supported the monophyly of several genera, including Moenkhausia, Megalamphodus, and Psalidodon. This study provides new molecular evidence for the taxonomic revision and germplasm resource evaluation of the family Acestrorhamphidae. However, the lack of whole-genome data, particularly for the genus Moenkhausia, remains a bottleneck, hindering in-depth research on adaptive evolution and speciation mechanisms. Future efforts should systematically conduct whole-genome sequencing and integrated analyses to enhance the understanding of the phylogeographic patterns and evolutionary history of this group.