Petal colour is one of the major characteristics that determine the ornamental value of lotus. To assess the contribution of different flavonoids to this character, composition and content of anthocyanins, flavones and flavonols were analysed through high performance liquid chromatography coupled with photodiode array detection tandem electrospray ionisation triple quad mass spectrometry in 108 lotus cultivars with red, pink, yellow, white and red/white pied petal colours. Totally, five anthocyanins and fourteen flavones and flavonols were detected and quantified. In general, the yellow, white and pied species hardly contained any anthocyanins; red cultivars contain more than pink cultivars. Among the five anthocyanins, malvidin 3-O-glucoside was the most abundant one in all the cultivars that contain anthocyanin. The fourteen flavones and flavonols belonged to four groups based on their aglycones. Except for the yellow cultivars, kaempferol-derivatives were the most abundant one. These data might be helpful in lotus breeding for different colours.