Bioinformatics analysis was conducted based on the acquired expressed sequence tags(ESTs)data from different tissues of Fenneropenaeus chinensis.A total of 10 446,2 690,1 067 and 1 282 original ESTs were obtained from cephalothorax,blood,eyestalk,and ovary of adult F.chinensis respectively.By clustering and assembling,3 454,1 053,406 and 544 unigenes were generated,and then annotated by searching in NR,GO,KEGG databases.The tissue specific transcripts were identified through sequence homology analysis and classified by GO annotation.The result indicated that specific transcripts in blood group were specifically enriched in the GO term of virion part,locomotion,rhythmic process,cell killing and multi organism process.Specific transcripts in eyestalk group were specifically enriched in the GO term of molecular transducer activity,response to stimulus,multicellular organismal process,pigmentation and biological regulation.Specific transcripts in ovary group were specifically enriched in the GO term of nutrient reservoir activity,reproduction,anatomical structure formation,transporter activity and establishment of localization.We also analyzed the highly expressed genes in each tissue according to the number of ESTs of each unigene.The result indicated that genes encoding peritrophin,elongation factor 1-alpha,thrombospondin and arginine kinase were widespread and highly expressed in tissues,suggesting that they were involved in a variety of important biological processes in shrimp.In addition,genes encoding penaeidin,cytochrome c oxidase and 14-3-3-like protein were highly expressed in blood group and genes encoding arrestin and rhodopsin were highly expressed in eyestalk group.For understanding the expressions of common genes,we analyzed genes related to peritrophin and peroxiredoxin,revealing that genes of peritrophin in F.chinensis were multiform and highly expressed.This result may provide reference for further functional study of peritrophin.