AbstractAnthocyanins are economically valuable phytochemicals of significant relevance to human health. Industrially extracted from multiple fruit and vegetable sources, anthocyanin yield and profiles can vary between sources and growing conditions. In this study, we focused on three purple-fleshed and one orange-fleshed cultivars of sweet potato—a warm-weather, nutritious crop of substantial interest to growers in northern, cooler latitudes—to determine the yield and diversity of anthocyanins and flavonoids. Acidified ethanol extraction of lyophilized roots yielded ~ 800 mg average anthocyanins/100 g dry weight from all three cultivars. UHPLC-DAD-Orbitrap analysis of sweet potato extracts identified 18 high-confidence, mostly acylated peonidin and cyanidin derivatives contributing to > 90% of the total anthocyanin signal. Further assessment of the untargeted Liquid Chromatography–Tandem Mass Spectrometry data using deep learning and molecular networking identified over 350 flavonoid peaks with variable distributions in different sweet potato cultivars. These results provide a novel insight into anthocyanin content of purple-fleshed sweet potatoes grown in the northern latitudes, and reveal the large structural diversity of anthocyanins and flavonoids in this popular crop.