Coat-epsilon protein (coat-ε) is a subunit of the coatomer complex that forms COPⅠ. To obtain the full-length sequence of coat-ε of Fenneropenaeus chinensis, we first acquired the sequences of 3' and 5' ends using rapid amplification of cDNA ends (RACE). The results were then spliced by DNAMAN to obtain the full-length 1402 bp sequence. The predicted 5' non-coding region (UTR) had 84 bp and the 3' non-coding region (UTR) had 310 bp. The open reading frame had 1008 bp that was supposed to encode 335 amino acids. The fragment including 230aa to 300aa belonged to the TPR superfamily. Signalp 3.0 server and TMHMM Server Version 2.0 analysis suggested that the amino acid sequence did not contain a signal peptide or a transmembrane structure. PSORTⅡ Prediction showed that coat-epsilon was probably located in mitochondria, cytoplasm, and endoplasmic reticulum. The phylogenetic tree analysis showed that coat-ε of F. chinensis was closely related to that of Arthropoda. We also analyzed the mRNA expression of coat-ε in different tissues with quantitative real-time PCR, and found that it was expressed in all tested tissues including appendage, hepatopancreas, epithelium, heart, stomach, intestine, eyestalk, muscles, gill, lymphoid organ and hemocytes. The expression level was the highest in muscles, followed by the gill and appendage. Our results provided important information for the functional study of coat-ε.