The genus Nemesia Vent. (Scrophulariaceae) comprises about 77 species, the majority of which are endemic to South Africa. Nemesia has garnered significant horticultural interest due to its diverse floral shapes, vibrant colours and ease of hybridization and cultivation. The genus was last revised in 1904 by Hiern and the only molecular phylogeny for Nemesia was published in 2008 by Datson and other researchers. Datson et al. grouped the 23 included species into 5 clades, highlighting evolutionary relationships and adaptive traits. Their ancestral state reconstruction suggested that multiple transitions occurred across a perennial life history in species occurring in the summer rainfall areas to an annual lifeform in species adapting to winter rainfall or seasonally dry conditions in the Cape Floristic Region and parts of the Karoo. It was hypothesised that Nemesia’s diversification may have been driven by climate change in the Cape Region during the Miocene and Pliocene. Our research aimed to generate a more comprehensive phylogeny incorporating as many Nemesia species as possible to deepen our understanding of the genus’s evolutionary history. The Bayesian Inference and Maximum Likelihood phylogenies were generated from gene regions ITS, ETS and trnL-intron, representing 48 species. The phylogeny was divided into two main clades with five subclades, each showing a clear geographic structuring, reflecting adaptations to distinct rainfall regimes. In this paper, we discuss the phylogeographic and morphological patterns within the clades and highlight the relationships of newly discovered taxa, offering fresh insights into Nemesia’s diversification.