Abstract: The complete mitochondrial D-loop fragment (937 bp total) of mud carp were successfully amplified by a pair of new designed primers. Seven hundreds and fifty bp mitochondrial D-loop fragment of 21 individuals (11 from sub-stock h, 10 from sub-stock q) of original population of mud carp were obtained after sequencing and alignment. Fifteen haplotypes were found in the 21 individuals. Twenty-nine nucleotide sites (4%) were variable. The genetic distance within the original population was 1.0%. The genetic distances were 1.2% and 0.9% within samples of sub-stock h and sub-stock q, respectively. In molecular phylogenetic tree constructed by UPGMA method, the 21 samples of the two sub-stocks mixed each other. Although phenotype vairiation existed between sub-stock h and sub-stock q, the two sub-stocks did not show special branches independently. So we believed that the two sub-stocks did not come from two independent maternal origins.