Flowering plants are characterized by the production of striking flower colours and these colours are primarily caused by the accumulation of pigments in cells of the floral organs. The extraordinary array of colours displayed in flowers relies on four main pigment groups: chlorophylls, carotenoids, flavonoids and betalains. With thousands of different compounds, flavonoids are the most diverse and widespread pigment group. They include coloured anthocyanins, aurones and chalcones, as well as many flavonoid compounds such as flavones and flavonols that are invisible to humans, but visible to most pollinators since they absorb ultraviolet light (UV). Flowers may exhibit homogenous colours produced by only one type of pigment or extremely complex colour patterns caused by the accumulation of several types of pigments in the same or in different floral organs. Here, we review the ecological biochemistry of pigments affecting flower colour. We also present data of flower colour variation and provide future research directions guided by the physiological functions of floral pigments.