Molecular divergence betweenGossypium klotzschianum andG. davidsonii was studied. The former is endemic to five of the larger islands of the Galapagos, whileG. davidsonii is restricted to the southern half of Baja California, approximately 2 500 km distant. A substantial body of genetic and taxonomic data suggests that these two species are related as progenitor and derivative. Interspecific hybrids are fully fertile, with no evidence of F2 breakdown and normal segregation of genetic markers. Allozyme analysis of 33 populations for 41 loci indicated that the allelic composition ofG. klotzschianum represents a subset ofG. davidsonii. Although genetic diversity is relatively restricted in both species, calculated measures demonstrate higher levels of genetic variability and greater population structuring inG. davidsonii than inG. klotzschianum. The interspecific genetic identity of 0.87 is typical for progenitor-derivative species pairs. Chloroplast DNAs were surveyed for variation with 25 restriction enzymes using hybridization probes that cover the entire chloroplast genome. No intraspecific and little interspecific variation was detected among 560 cpDNA restriction sites, representing sequence information for approximately 3200 nucleotides. Only 3 mutational differences distinguished the two species, resulting in a sequence divergence estimate of 0.09%. Divergence times were estimated from both the isozyme data and the cpDNA restriction site data. Although these estimates have several sources of error, both molecular data sets were congruent in suggesting that the two lineages diverged between 250000 and 700000 years ago. Accumulated evidence suggests that dispersal was from Baja California to the Galapagos Islands rather than the reverse, and most likely was mediated by trans-oceanic drift.G. klotzschianum may be the only species of the endemic Galapagos flora to have arisen from a northern Mexican progenitor.