Selective fishing is the successful capture of target species and size classes in a way that minimises bycatch, minimises damage to flesh, and maximises post-mortem (PM) value. We studied selective harvesting of blue cod Parapercis colias (Pinguipedidae) in central New Zealand, where it is captured mainly by commercial pot-fishing and recreational line-fishing. Potting with paua Haliotis iris (=abalone) guts selectively targeted large blue cod from localities that had six or more fish species and many small blue cod. Video observations of pot entries indicated that blue cod entered and left the pot throughout 30 min sets. Blue cod were observed by video to commence swimming when pot-hauling started. Observations of line-hooked fish indicated a characteristic spinning behaviour while hauling. Fatigue during harvesting is a major factor in reducing the PM quality and shelf-life of fish muscle. Despite the relatively benign nature of capture via pot, it appears that burst exercise during hauling and a brief flurry of flapping as the pot leaves the water is sufficient to compromise flesh quality. Fish that were fatigued during harvesting had a poorer peri-mortem ‘ATP potential’ than fish that had been tank-rested for a year and then harvested using rested harvesting techniques. Modifying the potting method by providing a reservoir of water reduced peri-mortem fatigue during capture but by an insufficient amount to significantly improve PM flesh quality. Blue cod flesh is compromised by pot capture, which is widely perceived as a benign harvesting method. In order to maximise value of blue cod, low-stress harvesting methods which take advantage of the behaviour of the fish are required.