As one of the first diverging branches of flowering plants, waterlilies, beautiful aquatic flowers, may hold the key to the origin of these remarkable organisms. The rise of the angiosperms (flowering plants) occurred suddenly, rapidly and mysteriously, prompting Charles Darwin to term it an ‘abominable mystery.’ Liangsheng Zhang and colleagues at Fujian Agriculture and Forestry University, Fuzhou, China, review how recent advances in genetic and genomic studies have narrowed down the first branching groups of the angiosperm family tree to three groups: a small New Caledonian tree, Amborella, a group of about 100 woody plant species known as Austrobaileyales, and the waterlilies. However, precise relationships among these groups remain unclear. The first waterlily genome to be sequenced will have great potential to shed light on the origin of angiosperms, as well as contribute to tools for breeding ornamental waterlilies.