I examined the influence of cyclic feeding regime on fillet yield and quality and their genetic architecture in rainbow trout (Oncorhynchus mykiss). Two lots of half-sib families produced in September and December were exposed to periods of reduced ration followed by increased ration. Fish fed cyclically reduced rations weighed less and had smaller fillets and body proportions relative to controls. They also had less estimated muscle and visceral lipid but also more proportional visceral mass. Lots and families within lots differed significantly for the majority of traits. Genotypic analysis with 23 microsatellite markers spanning 19 linkage groups detected QTL for all traits over multiple linkage groups that were not necessarily consistent between feeding regime and parental lot. Linkage groups RT-9 and 29 had the largest QTL effects for fillet composition traits and overall body size across the greatest number of parents sampled.