Abstract: Lotus (Nelumbo), as a basal eudicotyledon, is of great significance for studying the evolution and phylogeny of plants. It is also an economically important aquatic horticultural plant with ornamental, edible, and medicinal value. With the completion of genome sequencing, assembly, and annotation in the last decade, molecular level studies have greatly driven and expanded our understanding of all biological aspects of this species. In this review, we systematically discuss the latest advances in molecular biology studies of the lotus, with a focus on: (1) Recent progress in genomic research; (2) Genetic and multiomics studies of different horticultural traits and physiological processes; and (3) Characterization of key genes controlling important horticultural traits and their functions. Based on these, we also discuss current research challenges and future prospects.