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The complete of mitochondrial genomes in two kinds of Corbicula fluminea, black and yellow, are 17,293 bp and 17,068 bp in length, respectively. Both of them contain 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes (tRNAs), and one control region (CRs). The proportion of base-pairs in two kinds of C. fluminea are different, with A + T (68.78%) and G + C (30.17%) in black one as well as A + T (70.39%) and G + C (29.61%) in yellow one. Besides, the secondary structures in two kinds of clam, including trnS2, trnD, trnE, trnI, trnL1 and trnT, are various. This paper demonstrates the range of variation in mtDNA which could explore the relationship between the C. fluminea and geographical distribution.