It largely enriches transcriptome data of E. sinensis and indicates enormous advantage of high-throughput technology. Although a comparative transcriptome analysis of haemocytes from E. sinensis under normal condition and in response to Spiroplasma eriocheiris infection indicates certain microRNAs may be essential in interaction between host and pathogen, only miRNAs are identified and analyzed for the expression pattern. In our study, various immune genes and pathways are annotated from hepatopancreas of E. sinensis after immune challenge. The analysis increases molecular information and genomic resources of E. sinensis in response to microorganism stimulation. Toll pathway was initially identified in genetic screen of genes involved in early embryonic development of Drosophila and gradually studied of importance in innate immunity. In economic crustaceans, many genes related to Toll pathway, such as Spatzle, Toll, MyD88, Pelle and TRAF6, have been reported from shrimp, while only SpToll of Scylla paramamosain has been cloned and characterized from crab. In the present study, we are first to find various key members of Toll pathway in E. sinensis. This suggests the existence of putative Toll pathway in crab and indicates its crucial function in antimicrobial response. Moreover, different from mammalian Toll-like receptors directly Tulathromycin B functioning as a pattern recognition receptor to recognize pathogen-associated molecular patterns, DmToll of Drosophila melanogaster uses the cytokine-like molecule Spatzle as a ligand. In E. sinensis, identification of Spatzle in our study also suggests that the Chinese mitten crab Toll may be activated by functioning with Spatzle. In addition, in spite of different MyD88 variants in human, mice, chicken and other vertebrates, only a MyD88 variant gene is found in an invertebrate species L. vannamei. Here, we find one MyD88 sequence of E. sinensis that shows highest similarility to homolog from L. vannamei. This will provide a foundation for further study of MyD88 in crab. Folinic acid calcium salt pentahydrate Gram-negative bacteria-yielded diaminopimelic acid type peptidoglycan can be recognized by peptidoglycan recognition protein -LE and PGRP-LC receptor complex, which then activate IMD and cause activation of signaling cascade to trigger Relish. Experiments of Drosophila also reveal that infection by Gram-negative bacteria activates IMD pathway, but not Toll pathway. In this context, among different molecules relevant to IMD pathway, not only caspase and Relish previously reported are identified, but also IMD, dTAK1 and IKK are first found in microbial challenged E. sinensis. Similarly, LvIMD of L. vannamei and FcRelish of Fenneropenaeus chinensis are identified after immune challenge and characterization of them implies that they can induce expression of some antimicrobial peptides, which are integral components of innate immune system and exhibit great activities to defense against pathogens. Taken these reports together, investigation of principal component molecules will promote researching on innate immune mechanism and immune pathway of E. sinensis. A large number of molecules involved in JAK-STAT signaling pathway such as four JAKs, seven STATs and more than 30 cytokines are widely found in mammals. However, only SOCS and leptin receptor protein have been cloned from E. sinensis. In the present study, along with SOCS and LEPR, many other genes including CytokineR, JAK, STAT, downstream genes and regulatory molecules are first fully and systemically identified in crab. Considering different aspects of cell development and host response activated by JAK-STAT pathway, there is no surprise that lots of regulators are found to control this pathway. Expression and regulation of components in JAK-STAT pathway are also reported in transcriptome analyses of microbial infected Pseudosciaena crocea and Laodelphax striatellus.