The swimming crab (Crustacea:Decapoda:Brachyura) is a dominant species of portunid crab fisheries and an important economic species worldwide. The key performance traits of crustaceans and other aquaculture species are often depressed by inbreeding, especially if inbreeding effects accumulate too rapidly. Although previous studies have investigated the effects of inbreeding on the morphology, hatchability, and survival of crustaceans, little evidence is available that demonstrates that inbreeding affects crustacean physiology. Therefore, in order to investigate the effects of inbreeding on the oxidative phosphorylation of , cDNAs of the key subunit genes of the four mitochondrial respiratory chain complexes were cloned, sequenced using rapid amplification of cDNA ends (RACE), and then analyzed using bioinformatics technology. The full-length cDNA sequence of the Complex I core subunit genes was 1005 bp in length and contained a 705-bp open reading frame (ORF) that encoded a 234-amino acid polypeptide (GenBank:KY682717). The full-length cDNA sequence of Complex Ⅱ was 915 bp in length and contained a 540-bp ORF that encoded a 179-amino acid polypeptide (GenBank:KY406169). The full-length cDNA sequence of the Complex Ⅲ subunit (Cytc1) gene was 2371 bp in length and contained a 942-bp ORF that encoded a 313-amino acid polypeptide (GenBank:KY406171), and the full-length cDNA for the key subunit of Complex IV was 1171 bp in length and encoded 105 amino acids (GenBank:KY406170). In addition, homology and phylogenetic analyses revealed that the amino acid sequences of the four complexes were highly similar to those of closely related species and had higher conservation in evolution, and could be used as a reference for other marine organisms. The activities and mRNA expression of the four complexes in the hepatopancreas and heart mitochondria of were investigated. Results show that inbreeding reduced the activity of all four complexes and their respective subunit gene in the hepatopancreas (<0.05). Besides, Complex I, Ⅲ and IV activities and their subunit genes in heart were declined by inbreeding (<0.05). Furthermore, the elevated activity and expression of Complex Ⅱ in the heart may indicate that the ability to oxidize succinic acid and the level of aerobic metabolism in the crabs rose by breeding might because the dominant homozygous genes were accumulated during the family-based selective breeding programs. Therefore, it is clear that inbreeding gradually reduces the oxidative phosphorylation pathway and provides a reference for family-based selective breeding programs for .