Chloroplast DNA (cpDNA) restriction site and isozyme data were combined to explore the spatial-temporal influence of the Messinian desiccation in the Mediterranean on the disjunct distribution of Androcymbium gramineum in Almeria and Morocco (north and south of the straits of Gibraltar, respectively). Lack of evidence for different selective pressures, divergence time estimates based on the calibration of the isozyme molecular clock with the cpDNA data, the basal position of Almerian populations in the A. gramineum clade, and the much higher isozyme polymorphism in Almeria suggest that (i) only a southern European range of A. gramineum existed before the Messinian [approximate to 11.2 million years ago (Ma), in the middle Miocene] and (ii) the desiccation of the Mediterranean basin about 5.5-4.5 Ma induced the migration of A. gramineum from Almeria to Morocco (between 4.9 and 4.6 Ma, according to our time estimates). After the split into two allopatric units following the refilling of the Mediterranean, the major influence of drift associated with Plio-Pleistocene recurrent glaciation cycles and range expansions/contractions probably fostered the substantial interpopulation genetic differentiation observed within Almeria (CG(ST) = 0.41, average D-Nei = 0.185) and, to a lesser extent, within Morocco (CG(ST) = 0.24, average D-Nei = 0.089), but did not hinder the maintenance of considerable levels of genetic variation in either geographical area (A = 2.14, H-E = 0.230 and A = 1.90, H-E = 0.213, respectively).