Raspberries contain high levels of polyphenols that have been associated with health benefits in humans. The levels of polyphenols are under genetic control in that they vary between raspberry varieties, and are subject to modulation by environmental changes including abiotic stresses such as temperature, sunlight and rainfall. This study examined the total phenol content (TPC) and total anthocyanin content (TAC) in ripe fruit of progeny of a mapping population generated from a cross between the European red raspberry cv. Glen Moy (Rubus ideau var. idaeus) and the North American red raspberry cv. Latham (Rubus ideau var. strigosus) over a total of 5 seasons in two different growing environments. Corresponding measurements of antioxidant capacity (e.g. FRAP & TEAC) were also carried out. TPC was highly correlated with TEAC and FRAP over the entire dataset. The subset of anthocyanin content was genotype-dependent and also correlated with TPC though the proportion of anthocyanin compounds contributing to total phenolic pool varied from progeny to progeny. Quantitative trait locus (QTL) analysis was carried out, and key markers were tested for consistency of their effects over sites and years. Four regions, on linkage groups 2, 3, 5 and 6, were identified. These agree with previous QTLs from a previous study with data from a single season and show that the QTL effects were robust over a number of seasons. QTL areas that influence TPC but not TAC are of particular interest to boost the antioxidant capacity of raspberry fruits, which is often related to their bioactivies, and will be the focus of further studies.