The swimming crab, Portunus trituberculatus is a commercially important mariculture species in east coast regions of China. Molting is an important physiological process for the growth of P. trituberculatus and estrogen related receptor (ERR) may be involved in the molting regulation. The present study was designed to investigate the expression differences of estrogen related receptor (PtERR) in various tissues of Portunus trituberculatus during molting cycle by quantitative real-time PCR (qRT-PCR). The results showed that, for the tissue-specific expression analysis, the Y-organs and gill had the highest expression levels of PtERR, and the second highest expression levels were found in eyestalk and stomach, while the lower expression levels were found in three kinds of muscle tissues and the triangular membrane at stage C. The expression levels of PtERR varied significantly in any specific tissue at different stages of molting for 13 types of tissues. The expression pattern of PtERR-mRNA showed a significant increasing trend from stage AB to stage E in Y-organ; the pattern of "low-high-low" was found ifor the PtERR-mRNA of thoracic ganglia and eyestalk; the trend of "high-low-high" was found in mandibular organ; PtERR-mRNA had the significantly increasing trend in cheliceral muscle, appendage muscle and triangular membrane. However, the trend of "high-low-high" was found in abdominal muscle. In terms of digestive and metabolic organs, the expression levels of PtERR-mRNA increased firstly and then declined throughout the molting cycle in stomach, hepatopancreas and gill, and the peak value of PtERR-mRNA was detected at stage D; for intestinal tract, the highest expression level of PtERR-mRNA was found at stage D, and lower expression level was detected at stage C and stage E; finally, the expression level of PtERR-mRNA increased significantly in heart from stage AB to stage E, which was around two-fold increase for each stage. In summary, PtERR is mainly expressed in Y-organ, gill, eyestalk and stomach, which may be involved in the regulation of molting process, cell proliferation and energy metabolism.