Understanding how adaptive combinations of traits are maintained is a central question in evolutionary biology. Supergenes are clusters of genes that can maintain favorable trait combinations because they are inherited as a unit. Studying supergenes allows us to address fundamental questions on the origin and evolution of complex adaptations and the effects of suppressed recombination, and is therefore of broad significance. Distylous plants offer a particularly promising opportunity to study supergene evolution. In distylous plants there are two floral morphs that differ reciprocally in the placement of stigma and anthers. These favorable character combinations are maintained by a supergene, the distyly S-locus. While distyly has interested many generations of biologists, we still know little about the origins and molecular evolution of this supergene, and progress on this front has been hampered by the lack of molecular genetic data on the S-locus. Here, we aim to make full use of the latest advances in genome sequencing technology to bring the study of distyly into the genomic era. Specifically, we aim to test whether patterns of molecular evolution at the S-locus follow predictions based on sex chromosome theory, and investigate the genetic causes and population genetic consequences of recurrent loss of distyly. To do this, we will generate multiple de novo genome assemblies and conduct genetic and population genomic analyses in Linum, a classic system for the study of distyly. The high-quality genome assemblies produced during this project will form a valuable resource and pave the way for future studies of the molecular basis of adaptive floral differences first identified by Darwin. The results from this project are of great general importance for our understanding of the evolution of coadapted gene complexes, the genetic basis of convergent phenotypic evolution, and will shed new light on the important and fascinating phenomenon of supergenes.