Within the parasitic genus Cuscuta, three subgenera have been recognized based on characters of the styles and stigmas. Cuscuta subgenus Cuscuta, with free styles and conical to elongated stigmas, is the most diversified in the Old World with about 25 species. We present the first phylogenetic study of the subgenus using nuclear ITS rDNA and chloroplast trnL intron sequences. Sequences of almost all species of the subgenus were obtained and several individuals of particular taxonomic difficulty or wide geographical distribution were sampled. Both maximum parsimony and Bayesian analyses were performed to evaluate the monophyly of the sections previously accepted in Yuncker's monograph and to investigate phylogenetic relationships between the species. The monophyly of the subgenus could not be tested with our sampling but using three species of subgenus Monogyna as outgroup, the South African section Pachystigma was sister to the remaining species of subgenus Cuscuta. Section Epistigma plus C. capitata are resolved as monophyletic in all analyses. The distinctive C. babylonica was sister to that clade on the ITS trees but it was not resolved on the trnL trees. Two monophyletic groups within section Cuscuta, first identified here, included the species of tropical African distribution in one case and C. europaea, C. approximata, and C. balansae in the other. Factors influencing the taxonomic difficulty of many species in the subgenus include lack of morphological characters, parallelism and gene flow between closely and not so closely related species. Evidence of reticulation events or within species recombination were obtained by both polyphyletic intra-individual ITS sequences and conflicting topologies of the nuclear and plastid trees.