Carnitine acetyltransferase (CAT) is an enzyme that has effect on short-chain fatty acids. In this study, the open reading frame (ORF) of CAT was cloned from Chinese mitten crab Eriocheir sinensis by PCR, to analyze the CAT tissue-specific expression and the changing patterns of CAT expression levels in hepatopancreas and ovaries during different stages of ovarian development by quantitative real-time PCR (q-PCR). The results showed that the ORF of CAT was 1 929 bp in length and encoded 642 amino acids (Fig. 1) without transmembrane domain and signal peptide, with the predicted protein containing an Acyltransferases ChoActase conserved domain (40﹣56 aa) and a typical Carn-acyltransf superfamily domain (43﹣626 aa) (Fig. 2). For either males or females, CAT expressed in all detected tissues. In males, higher CAT expression levels were detected in hepatopancreas and muscle (Fig. 4). In females, the highest expression level was obseeved in hepatopancreas, followed by the ovaries and muscle (Fig. 5). The observed changes of CAT expression levels in hepatopancreas and ovaries significantly varied in different ovarian development stages (P < 0.05) (Fig. 6, 7), suggesting that CAT may play an important role in E. sinensis during its ovarian development.