To identify distinctive genes associated with immunity in the Chinese mitten crab (Eriocheir sinensis), an expressed sequence tag (EST) library was constructed from haemocytes of this economically important species. 3118 clones were unidirectionally sequenced and analyzed by homology searches against sequences in the GenBank, KEGG and Uniprot. Significant homology (BLASTX, e-values < 10^− 5) to known genes was found in 488 of the 1039 unique sequences. The automatic functional classification based on KEGG and Gene Ontology revealed 26 putative immune-related genes (2.5% of all unique sequences, 18.9% of all ESTs). These 26 genes coded for enzymes and proteins in the clotting and prophenoloxidase-activating system, antioxidative enzymes, antimicrobial peptides, and pattern recognition molecules. The existence of these molecular processes in the activation of cellular defense in crab has not been previously reported. According to EST abundance, the major immune-related genes were the Kazal-type proteinase inhibitor (337, 11.1% of all ESTs) and the C-type lectin (72, 2.4%). The EST sequences of mitten crab haemocytes provide important information for understanding the evolution of the immune system among crustaceans in general. This study lays the groundwork for development of molecular markers related to disease resistance in the crab.