日本花棘石鳖（Liolophura japonica）是无脊椎海洋动物，在我国东南海地区分布较为广泛，具有较高的食用及药用价值。本研究以浙江南麂列岛、福建东山岛和广东汕尾日本花棘石鳖作为研究对象，利用细胞色素c氧化酶亚单位I（COI）、线粒体16S核糖体RNA基因（16S rDNA）和细胞核28S 核糖体RNA基因（28S rDNA）为分子标记，对其遗传结构、遗传多样性和种群历史动态进行了分析。主要结果如下：日本花棘石鳖的碱基序列特征和遗传多样性指数结果，显示出16S rDNA基因较为保守，COI基因存在较为丰富的变异，更适合种群遗传学发面的研究。Fst值、邻接树和单倍型网络关系图表明三个地理种群间，没有出现明显的遗传分化，可能是日本花棘石鳖三个地理种群间基因交流比较频繁的原因。依据Tajima's D和Fu’s Fs中性检验的结果和核甘酸不配对分析图，推断日本花棘石鳖未经历过群体扩张。

Liolophura japonica is invertebrate Marine animals, which are widely distributed in the southeast coastal areas of China, has high edible and medicinal value. This study focuses on Liolophura japonica in Nanji islands of ZheJiang Province, Dongshan islands of FuJian Province and Shanwei of GuangDong Province, using the Cytochrome Oxidase Subunit I (COI) 、16S rDNA genes and 28S rDNA genes as molecular markers, and analysing investigation of genetic diversity、genetic structure and historical dynamic pattern. The main results were as follows: according to the base sequences and the genetic diversity index of Liolophura japonica, we find out that 16S rDNA genes are relatively conservative, while COI genes reveal abundant genetic diversity, which means COI genes are more appropriate to be molecular markers for population genetics research. Fst value, the NJ tree and haploidtype network show that there are no obvious genetic differentiation between the three geographical populations, Which may result of the frequent gene exchanges between populations. According to Tajima 's D and Fu' s Fs neutral inspection results and the analysis chart of nucleotide mismatch distribution, it can be presumed that there is no population expansion.