The scalloped hammerhead shark (Sphyrna lewini) is circumglobally distributed along continental margins and oceanic islands in tropical waters. With the development of fishery resource, S. lewini is one of the most affected and ecologically important species. It is very important to investigate the genetic variance and population structure of this species. However, there are no genetic investigations for this fish in China. In the present study, thirty-four individuals were collected to analyze the genetic diversity and genetic structure for this species. A 548 base pair (bp) fragment of the hypervariable portion of the mtDNA control region was sequenced and sequences were edited and aligned. The fragments revealed 11 polymorphic sites, which defined 5 haplotypes. The results of present study showed that haplotype diversity, nucleotide diversity and mean number of pairwise differences of Rizhao population (h=0.6000±0.1305; π=0.0046±0.0031; p=2.5333±1.4856) were a little higher than those of Xiapu population (h=0.5109± 0.0955; π=0.0024±0.0017; p=1.2899±0.8373). A Neighbour-Joining (NJ) tree of the control region haplotypes was constructed based on the outgroup S. zygaena and two haplotypes from East Pacific which were downloaded from NCBI. Two haplotypes from East Pacific were clustered with three haplotypes from the present study and two lineages were distinguished by 1.6% sequence divergence. The pairwise fixation index F_st=－0.047 (P=0.914) revealed no significant genetic differentiation between these two populations. The exact test of population differentiation (non-differentiation exact P values) following sequential Boferroni correction showed that no significant differences (P<0.01) existed among between two populations, which supported null hypothesis. The mismatch distribution analysis of all the S. lewini sequences was bimodal, and one small mode corresponded to internal clade comparisons and the other to differences between individuals among clades. Low levels of genetic diversity in Chinese Coast Sea for S. lewini may be a consequence of small effective population size which restricted gene flow. The results of present study provided a deeper understanding of the processes that led to existing levels and patterns of genetic diversity.