Evolutionary mechanisms, such as whole genome duplication (polyploidy) has been noted to alter morphology and reproductive strategies of plant species, leading to the generation or the loss of species. Rhodohypoxis (Hypoxidaceae) is a small Drakensberg near endemic genus containing six species, one of which is Rhodohypoxis baurii. Rhodohypoxis baurii contains three morphologically distinct varieties, each with varying ploidy-levels (2x, 3x and 4x). Gene flow has been noted to occur between varieties as well as ploidy levels making R. baurii an ideal system to evaluate whether polyploidy can lead to lineage divergence or homogenization via shifts in reproductive strategies. To evaluate potential reproductive barriers, a total of 231 crosses were performed both between and within varieties and ploidy-levels, of which 113 produced 1530 seeds. Pollen viability was compared among varieties and ploidy levels to assess if reproductive barriers were pre-zygotic. Genetic differentiation and gene flow were quantified both among the varieties and ploidy-levels across 11 populations using 12 microsatellite markers. Thirty vegetative, floral, and reproductive traits were measured across 124 herbarium specimens and 43 individuals housed in the greenhouse. Ploidy levels were estimated using flow cytometry and compared to morphology, genetic differentiation and reproductive strategies. Rhodohypoxis baurii polyploid individuals show a shift away from sexual reproduction to asexual reproduction as polyploid intra-ploidy crosses showed lower seed sets and germination rates than diploid intra-ploidy crosses. Furthermore, all polyploid R. baurii individuals showed higher rates of clonal reproduction than diploid individuals. A latitudinal ploidy gradient was found across sampled populations that correspond with shifts in reproductive strategy, and changes in the extent of gene flow. Population genetic structure coincided primarily with geographic localities, with diploid Northern Drakensberg populations comprising similar allelic diversity to each other, but differed from the tetraploid Southern Drakensberg populations. Conclusively, decreased gene flow facilitated by polyploidy, shifts in breeding systems and geographic isolation are likely contributing to both species diversification and homogenization in this lineage.