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Phylogenetic analysis of chloroplast DNA (cpDNA) restriction site variation supports a close genetic relationship between the Southwest Asian Senecio flavus subsp. breviflorus and the North American S. mohavensis. The intercontinental disjunct distribution of these two desert annuals may have originated via long distance dispersal. The chloroplast genomes of the Southern and North African S. flavus subsp. flavus and subsp. breviflorus differ by at least ten restriction sites, while at most two restriction sites differentiate the cpDNA genomes of subsp. breviflorus and the outgroup S. squalidus. This suggests that the cpDNA genome of S. flavus subsp. breviflorus may have resulted from introgression and chloroplast capture with a Mediterranean species related to S. squalidus. This hypothesized introgression could account for the morphological distinctiveness and duplicated isozyme loci of S. flavus subsp. breviflorus relative to subsp. flavus.