Dalian sea cucumber, Yantai sea cucumber, and Weihai sea cucumber, which belong to Apostichopus japonicus, are protected as geographical indications in China based on their high nutritional values and medical propertys. The 26 samples, including Dalian sea cucumbers (9 samples) in Liaoning province, Yantai sea cucumbers (9 samples), and Weihai sea cucumbers (8 samples) in Shandong province, were individually collected from the designated geographical sea areas and the genetic relationships and DNA polymorphisms were evaluated by random amplified polymorphic DNA technology and gene segments sequencing. The RAPD dendrogram showed that the genetic diversity of the three types of sea cucumbers was rich. The neighbor-joining tree shows that the genetic relationship of the samples from the adjacent sea areas is closer. It demonstrates that the gene characteristics of sea cucumbers from different sea areas were obvious and the genetic diversity analysis by RAPD-PCR can be used as a rapid method for geographical discrimination.