In order to study the molecular regulatory mechanism of Marsupenaeus japonicus under high nitrite stress the hepatopancreas of M. japonicus from both the high nitrite stress groups and the control groups were sequenced. The transcriptome of hepatopancreas of Marsupenaeus japonicus was analyzed by the new generation of high-through-put sequencing technique of Illumina, and the functional genes associated with high nitrite tolerance of Marsu penaeus japomicas was explored through the assembly of high quality sequences, gene annotation and classification. The results were as follows: a total of 920 785 608 clean reads were obtained from 10 libraries with the data volume 6.48G~7.34G and Q30 more than 93.07%.46 308 unigenes and 1 833 bp N50 were obtained by Trinity software. Compared with the control group, 593, 606, 1 089, 497 and 988 DEGs were obtained and DEGs were annotated to speculate the pathways and genes related to immunity and metabolism. The expression of nine differential genes speculate(DPD，ABCH，ProPOb, ACADL, CYP2J，PAT4, BHMT, CLEC and PEPCK ) was detected by qPCR, and the expression level was consistent with the trend of RNA seq. This study enriched the prawn cDNA database information of prawn, andlaid a foundation for the molecular mechanism of Marsu penaeus japonicus under high nitrite stress.