Discerning the basis of phenotypic and genotypic differences within and between taxa is crucial for understanding the evolution of species, subspecies or varieties and races. In this dissertation, I have presented three studies, which use morphological characters and genetic Amplified Fragment Length Polymorphisms (AFLPs) to differentiate cytotypes, populations and species of the genus Xanthisma. The first study is aimed at clarifying the species status of Haplopappus ravenii, which has been considered to be a separate species by some taxonomists and a race of Xanthisma gracile by other researchers. Considering the morphological species concept and the genotypic cluster definition of a species, there was insufficient distinction in either dataset to support these taxa as distinct species. It was found that H. ravenii is more appropriately classified as a a cytotype or a race of X. gracile. In the second study, the genetic structure of X. gracile was quantified across populations occupying distinct habitat types (desert, grasslands, and pinyon juniper woodlands) in order to test the hypothesis of local adaptation and to determine the potential for intraspecific divergence. Samples from desert habitats showed higher genetic divergence than samples in the other two habitats. This study is indicative of local adaptation of populations and that changes in climate and habitat play a very important role in the genetic differentiation of plant systems. The third study evaluated the taxonomy of Xanthisma spinulosum and three of its subspecies that co-occur in Arizona. Herbarium specimens representative of the three subspecies were used to test for significant morphological and genetic divergence that would support their recognition. The morphological characters originally utilized by taxonomists who named these taxa were not significantly different among the three taxa. This finding was further supported by the molecular data, suggesting the presence of one contiguous species. This dissertation aims at stressing the importance of taxonomic status and understanding the role that environment can play on shaping differentiation between taxa.