The article presented the results of the first regular population study of triploid hybrids of crucian carp and common carp by sequencing the tRNA2Thr gene,tRNA2Pro gene ,and partial control region of mitochondrial DNA (mtDNA). The 26 sequenced fragments ranged from 837 to 839 bp in length. The termination associated sequence (TAS) motifs,central conserved sequence blocks (CSB2F ,CSB2E ,CSB2D),and conserved sequence block (CSB1) were identified in the mtDNA control region.Most heteroplasmic fish had 3-5 TAS repeat units. The above sequences from 26 triploid hybrids were detected 65 polymorphic sites,yielding 8 haplotypes. Sequence divergence among different haplotypes ranged from 0.1 % to 613 %. This study provided some invaluable information for the reproducibility and genetic improvement of triploid hybrids.