The South China Sea (SCS) surrounded by the first island chain is a semi-enclosed sea linking the Indian and the Pacific Ocean. The population genetic features of the two most important economic species, Yellowfin tuna (YFT, Thunnus albacares，17 adults and 44 juveniles) and Big-eye tuna (BET, T. obesus，22 adults and 4 juveniles) in SCS（11~12°N, 15°N; 110~112°E）, have been analyzed based on the partial mitochondrial D-loop sequences. Our data supported the following conclusions: (1) two species both were high nucleotide variation with very high Haplotype diversities (Hd＞99%), while the evidence from fixation indexes, and cluster trees showed the population diversity of BET was higher than those of YFT; (2) For BET and YFT, the strongest gene flow exits between populations in SCS and the Indian Ocean were 51.638 and 261.28010, then the Pacific by 10.8688 and -50.80181, respectively; (3) both species obey the sudden expansion model. Contrast with the unimodal of YFT, the mismatch distribution of BET, as well as the SCS population, were bimodal. Moreover, the spanning time of SCS population of BET was later inferred from the Tau (=7.902) with biggest spanning scale (θ1/θ0=99999/14.752). This results should be basic file for fisheries management, fishing quotas determination as well for aquaculture of tuna.