Technical Abstract: Claviceps purpurea is an important pathogen of grasses and source of novel chemical compounds. Three groups within this species (G1, G2, and G3) have been recognized based on habitat association, sclerotia and conidia morphology, and alkaloid production. These groups have further been supported by genetic markers, suggesting this species may be more accurately described as a species complex. In this study, we used a multi-gene approach to test for speciation within C. purpurea using DNA sequences. We found that C. purpurea sensu lato appears to be in the early stages of speciation. The G1 types are significantly divergent from the G2/G3 types based on each of the three loci and the combined dataset, whereas the G2/G3 types are more integrated with one another. Our results suggest that these fungi are in the process of speciation and we argue that this process is driven by adaptations to ecological habitats; G1 isolates are associated with terrestrial grasses, G2 isolates are found in wet and shady environments, and G3 isolates are found in salt marsh habitats. All divergent ecotypes can coexist in sympatric populations with no obvious physical barriers to prevent gene flow. However, our results suggest that no genetic exchange is occurring between these divergent groups.