Abstract: In this study, homologous cloning and semi-quantitative RT-PCR technologies were used to clone the fragments of NLR genes and to detect their expression patterns in tissues of sea urchinStrongylocentrotusintermedius. The primers were designed according to the homology alignment of NLR genes from purple sea urchinS.purpuratus, and 9 fragment groups of NLR genes were obtained from the sea urchin, by sequencing of 10 clones for each group. Then bioinformatic analysis of these genes was conducted by the method of Blast, finding the diversity of cDNA sequences and amino acid sequences of these NLR genes. Also, the RNA was extracted from different tissues in the sea urchin, and the expression of NLR genes was analyzed by semi-quantitative PCR in different tissues of the sea urchin after reverse transcription. The results showed that 9 fragment groups of NLR genes were all expressed in coelomocytes (CL), membrana peristomialis (WK), intestines (GT), tube-feet (GZ), and gonad (GD) at a high level, the maximum in membrana peristomialis and gonad, indicating that NLR gene family plays an important role in the congenital immune system of the sea urchin, with different expression. The findings will provide the foundation for further study of NLR genes in the sea urchin.