Truncatelloidea is the richest and most diverse group within Mollusca. Both morphological and molecular studies have sought to resolve its phylogenetic framework; however, the phylogenetic relationships among some lineages remain controversial. To explore the phylogenetic relationships within Truncatelloidea, this study presents a mitochondrial phylogenomic framework, reconstructed from a dataset integrating 15 newly sequenced mitochondrial genomes with existing data from NCBI and encompassing 20 genera from 11 families. Both maximum likelihood and Bayesian inference analyses supported that the superfamily was resolved into two major clades (I and II). Within Clade I, Assimineidae and Stenothyridae form a sister group, while Baicaliidae and Bithyniidae are distantly related to the remaining families. Within Clade II, Aenigmula and Clenchiellidae form a sister group, with Iravadiidae occupying the most basal position. Furthermore, the monophyly of all other families and genera is strongly supported except for Assiminea within Assimineidae. Additionally, based on morphological observations, phylogenetic analyses of COI, 16S rRNA, and 28S rRNA gene fragments, species delimitation methods (ABGD, ASAP, bPTP), and genetic distance calculations of the collected Truncatelloidea specimens, a new species, Aenigmula sinensis sp. nov., was identified and described, while an undetermined species, Aenigmula sp., was recorded. The findings strongly support the recognition of Aenigmula as an independent lineage, offering more comprehensive morphological character descriptions and molecular evidence for this genus.