Raspberry (Rubus idaeus) fruit colour was assessed in the Latham x Glen Moy mapping population using a colour meter and visual scores over three seasons and three environments. The colour measurements were found to have high heritability, and stable QTL were identified across the environments and seasons. Anthocyanin content has previously been shown to be the major contributor to fruit colour in red raspberry. Major structural genes (F3'H, FLS, DFR, IFR, OMT, GST) and transcription factors (bZIP, bHLH, MYB) influencing flavonoid biosynthesis have been identified, mapped and shown to underlie QTL for quantitative and qualitative anthocyanin composition. Favourable alleles for selected traits were identified for aspects of fruit colour and partitioning of individual pigments.