Abstract Consumption of raspberries promotes human health through the intake of pharmaceutically-active antioxidants, including cyanidin and pelargonidin anthocyanins. These are products of flavonoid metabolism and also pigments that confer colour to fruit. Breeders may wish to influence fruit anthocyanin content for nutritional health and quality benefits through modern breeding utilising DNA polymorphisms: marker assisted breeding (MAB). High performance liquid chromatography (HPLC) quantified eight anthocyanins cyanidin and pelargonidin glycosides: -3-sophoroside, -3-glucoside, -3-rutinoside and -3-glucosylrutinoside across two seasons and two environments in progeny from a cross between two Rubus subspecies, Rubus idaeus (cv. Glen Moy) x Rubus strigosus (cv. Latham). Significant seasonal variation was detected across the pigments but less so for the different growing environments within a season. The eight antioxidants mapped to the same chromosome region on linkage group (LG) 1, across both years and from fruits grown in the field and under protected cultivation. Seven antioxidants also mapped to a region on LG 4 across years and for both field and protected sites. A chalcone synthase (PKS 1) gene sequence mapped to LG 7 but did not underlie the anthocyanin QTLs identified. However other candidate genes including bHLH, NAM/CUC2 like protein and bZIP transcription factor underlying the mapped anthocyanins were identified.