Background/Objectives: The monotypic genus Araiocypris is currently classified in Xenocyprididae, yet its familial placement has long been controversial and lacks sufficient molecular phylogenetic support. Mitogenomic resources for the family Tanichthyidae remain limited, and the phylogenetic relationship between Araiocypris and tanichthyid species remains unexplored. This study was conducted to re-evaluate the taxonomic status of Araiocypris and characterize the mitogenomic evolution of Tanichthyidae. Methods: The complete mitochondrial genomes of Tanichthys huidongensis and Araiocypris batodes were sequenced, assembled and annotated. Comparative mitogenomic analyses were performed across seven Tanichthyidae species. A maximum-likelihood phylogenetic tree was reconstructed using concatenated sequences of 13 protein-coding genes and 2 ribosomal RNA genes to clarify the phylogenetic position of Araiocypris. Results: Based on mitochondrial phylogenomic evidence, phylogenetic reconstruction strongly supports the reassignment of A. batodes from Xenocyprididae to Tanichthyidae, as it nests within the Tanichthyidae clade and forms a sister group with the genus Tanichthys. Genetic divergence analysis confirms the validity of Araiocypris as a distinct genus. Tanichthyidae mitogenomes display highly conserved architecture with the typical vertebrate gene order. All protein-coding genes undergo strong purifying selection, with cox1 showing the slowest evolutionary rate. Conserved structural domains including CSB-F, CSB-E, CSB-D and CSB1–3 were identified in the control region. Conclusions: This study provides solid mitogenomic evidence for the familial reclassification of Araiocypris and systematically reveals the evolutionary patterns of Tanichthyidae mitogenomes, offering an important reference for further taxonomic and phylogenetic studies of Cypriniformes.