While sex determination has been extensively studied in animals, the origin and early evolution of sex chromosomes in plants remain poorly understood. Magnolia kwangsiensis, an early-diverging dioecious flowering plant, provides a unique opportunity to investigate sex chromosome evolution at early stages. Here we generated phased chromosome-level genome assemblies for male and female M. kwangsiensis individuals (~2.4-2.5 Gb of 19 chromosomes) and uncovered a nascent XY sex chromosome system. The