Abstract: Doubly uniparental inheritance (DUI) of mitochondrial DNA, a rare exception to the strict maternal inheritance typical in animals, occurs only in certain bivalve families and is characterized by distinct gender-associated mtDNA lineages through males (M-type) or females (F-type). Due to frequent undetection, M-type sequences remain underrepresented in GenBank, impeding deeper understanding of DUI phenomenon. In this study, we sequenced and analyzed the complete M and F mitogenomes of the freshwater mussel Lepidodesma languilati. The complete mitochondrial genome sequences of the F-type and M-type in L. languilati were 15768 bp and 17008 bp in length, respectively. Both exhibited a strong AT bias, with an A+T content of approximately 64%. Each genome encoded 37 genes, including 13 protein-coding genes (PCGs), 22 tRNAs, and 2 rRNAs. Twenty-six genes were located on the light strand and 11 on the heavy strand. Structural defects were observed in several tRNAs: both F and M-type trnS genes lacked the TψC loop, and the M-type trnY gene lacked the DHU arm. Relative synonymous codon usage (RSCU) analysis showed that TTT was the most frequently used codon in both F-type (RSCU=1.55) and M-type (RSCU=1.63) genomes. Phylogenetic analysis clearly demonstrated that the F and M-type mitochondrial genomes form two distinct monophyletic clades. Selective pressure analysis suggests atp8 as a potential sex-differentiation-related gene. In summary, this study provides the first comprehensive characterization of the structural differences, base composition, codon usage patterns, and non-coding region organization between the F and M-type mitochondrial genomes of L. languilati, supporting a pattern of parallel evolution between the two genomes in phylogenetic context. These findings not only provide fundamental data for further comparative and applied studies of the mitochondrial genome in this species, but also contribute to a deeper understanding of the DUI phenomenon.