Terrestrialization is an important evolutionary process that plants experienced. However, little is known about how land plants acquired aquatic growth behaviors. Here, we integrate multiproxy evidence to elucidate the evolution of the aquatic plant duckweed. Three genera of duckweeds show chronologically gradual degeneration in root structure and stomatal function and a decrease in lignocellulose content, accompanied by the contraction of relevant gene families and/or a decline in their transcription levels. The number of genes in main phytohormone pathways is also gradually decreased. The coordinated action of genes involved in auxin signaling and rhizoid development causes a gradual decrease in adventitious roots. Additionally, the significant expansion of the flavonoid pathway is related to the adaptation of duckweeds to floating growth. This study reconstructs the evolutionary history of duckweeds, tracing its journey from land back to water — a reverse trajectory of early land plants.