The backbone of interpreting patterns of relationship and inferring processes of evolution must be done within the context of phylogeny. Early efforts in phylogenetic reconstruction in Melampodium in the 1970s were based on morphology and cytology. The resolution of evolutionary relationships among all species was greatly improved with nuclear and plastid DNA sequences, and at the populational level among the three species of the white-rayed complex with AFLPs (amplified fragment length polymorphisms) and plastid haplotypes. The newly reconstructed phylogenies have provided a structure within which to examine chromosomal evolution and interpret biogeography. Results have clarified that three species of Sect. Alcina, previously held together primarily by sharing the same chromosome number of n = 11, are not closely related.