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Genetic patterns were examined in five populations of North American Cleistes with three sources of molecular data: amplified fragment length polymorphisms (AFLP), DNA sequencing, and plastid microsatellites. Populations of C. bifaria were sampled in four areas of the south-eastern US: the coastal plains of Florida and North Carolina and the mountains of North Carolina and West Virginia. A population of C. divaricata sympatric with the North Carolina coastal plain C. bifaria was also sampled. Analysis of the three types of molecular data resulted in the same relationships among the five sampled populations. The coastal plain population of C. divaricata was consistently grouped with the C. bifaria populations from the mountains of West Virginia and North Carolina, and the two coastal plain populations of C. bifaria formed a separate group, results not supporting the existing concepts of species relationships. For future studies, greater sampling of C. divaricata populations and more detailed morphological and phenological studies are recommended for better characterization of the diversity within North American Cleistes.