Carex subg. Vignea is a distinctive taxon characterized by sessile, bisexual inflorescence units, distigmatic flowers, and the lack of cladoprophylls. Evolutionary relationships within this subgenus were examined using amplified fragment length polymorphism (AFLP) data alone and in combination with nrDNA ILS and ETS 1f (external transcribed spacer 1 fragment) sequences. Parsimony and Bayesian analyses of the combined dataset show the atypical C. gibba (tristigmatic flowers, cladoprophylls) to be sister to the remainder of subg. Vignea. All gynaecandrous sections are monophyletic, with gynaecandry having arisen multiple times. In contrast, androgynous sections are largely polyphyletic, with most clades comprised of disparate assemblages of taxa that are often difficult to correlate with morphology or geography. Bootstrap values/posterior probabilities support terminal and early diverging clades, but support along the backbone of all trees is poor. Trees produced using Bayesian methods have a greater number of supported branches than those produced by parsimony, suggesting that the high levels of homoplasy observed within the combined dataset may be better addressed by a model-based method. Bayesian analysis of the AFLP data alone results in trees that are topologically similar to those produced by a Bayesian analysis of the combined data. Parsimony trees generated using AFLP data alone are topologically different from other phylogenetic reconstructions. In groups such as subg. Vignea, which may be recently evolved, AFLPs provide a rich source of highly variable characters that give good support for terminal clades. However, high rates of homoplasy will likely limit their application in higher-level phylogenetic studies in Carex.