In high elevation habitats of the Peruvian Andes a new population of Microseris (Asteraceae, Lactuceae) related to the single South American species, M. pygmaea, recently was discovered. Microseris pygmaea occurs at lower elevations in Chile and has originated after long-distance dispersal from a Californian progenitor. Differences in flowering traits and habitat preferences of the new population raised the question of its precise phylogenetic affiliation. The analysis of the nuclear rDNA internal transcribed spacer (ITS) region of all Microseris species revealed the Peruvian plants as part of the Chilean M. pygmaea clade. Molecular, ecological, and physiological data resulted in an interpretation of the Peruvian population as derived from Chilean progenitors instead of being remnants of stepping-stone dispersal from North America through the Andes to Chile. Differences in ITS sequences found in this study compared to earlier ones were explained by the occurrence of two different rDNA clusters in the genome of Microseris, which were preferentially amplified by differences in the PCR protocols.