The island of Madagascar is known for its rich fauna and flora, and is an ideal area to study species and speciation (Vences et al., 2009), especially species in the Hibiscus tribe (Koopman & Baum, 2008). The island contains unparalleled levels of endemism and species diversity, making it one of the greatest biodiversity hotspots in the world (Goodman & Benstead, 2005). The three morphologically distinct plant species in the genus Megistostegium will be used to study speciation. Previous research has shown that all three species are, genetically, very similar (Koopman & Baum, 2011; Callewaert, 2014). This research aims to use additional molecular data to determine how the three morphologically distinct species in the genus Megistostegium are related. Genomic DNA will be extracted from 110 individual plants, representing one to five populations per species. Individual plants will be sequenced using RADseq next-generation sequencing methods. Genetic variation will be summarized across all individuals, populations, species, and across geographic space. Phylogenies will be constructed to understand how the three species are related.