Gossypium gossypioides has been a perplexing entity, with morphological and molecular studies yielding conflicting interpretations of affinity to other American cottons. Herein, we reevaluate the evolutionary history of this enigmatic cotton and its relationship to key species from the New and Old World, using 15.4 kb of DNA sequence. This synthesis shows that chloroplast DNA (6.3 kb), nuclear ribosomal internal transcribed spacers (0.7 kb), and unique nuclear genes (8.3 kb) each yield conflicting resolutions for G. gossypioides. Eight low-copy nuclear genes provide an unexpected, nearly-unanimous, resolution of G. gossypioides sister to all American diploid cottons. Due to the evolutionary independence of these estimates, we suggest that this consensus accurately reflects the evolutionary history of G. gossypioides. In contrast, cpDNA resolves G. gossypioides as sister to the Peruvian G. raimondii, while ITS places G. gossypioides in an African (rather than an American) clade. We suggest that the conflicting phylogenetic signal arose from two separate hybridization events in the ancestry of G. gossypioides, one involving a divergent African cotton unrelated to the A-genome of polyploid cotton (resulting in nuclear repetitive DNA introgression; Wendel et al., 1995), and a second hybridization event involving a Mexican species that resulted in chloroplast introgression. Gossypium gossypioides provides a striking example of the phylogenetic complexity that can arise from multiple reticulation events. This example testifies to the necessity of using multiple molecular markers in phylogenetic inference and illustrates the insights that may derive from using a combination of single-copy nuclear, cpDNA and nuclear repetitive sequences.

Key words: cotton, Gossypium gossypioides, hybridization, Malvaceae, phylogenetic incongruence