Running head: Allopatric cryptic speciation and population structuring in skates-2-ABSTRACT Aim Geographical (allopatric) speciation is a dynamic process whose footprints in the living world are a continuum of stages of increasing divergence. Geographical speciation can also contribute to the evolution of marine taxa. This study looked for two of these evolutionary stages (i.e. structured populations and sibling species) in the diversification patterns of two Atlantic skates (Raja, suborder Rajoidea) which exhibited high morphological and ecological conservativism. Location E Atlantic, Mediterranean, W Indian Methods Phylogeographical and population genetic analyses were performed by surveying DNA variation of 10 population samples assigned to the European Raja clavata and to the S African R. straeleni. Polymorphisms were detected by sequencing a mtDNA control region (CR) fragment and genotyping amplified fragment length polymorphism (AFLP) loci. Several statistical tests were used to explore genetic differentiation and population demography. Results CR haplotypes clustered in two clades consistent with taxon zoogeography. Mean sequence divergence between allopatric taxa amounted to 2% and Bayesian estimate of the time of the most recent common ancestor dated their separation between 0.155 and 1.3 Myr. Isolation-by-distance between European and S African demes was inferred from a significant correlation between coastal and genetic distances at AFLP loci. Null or low gene flow estimates suggested reproductive isolation between allopatric taxa. After separation, taxa have expanded moderately since 30-45 Kyr. Geographical subgrouping of CR haplotypes and significant genetic heterogeneity of samples at both markers featured the Atlantic and Mediterranean thornback skates, revealing pronounced levels of population structuring in this widely distributed taxon. Main conclusions In spite of the pronounced morpho-anatomical conservativism, R. clavata and R. straeleni are allopatric sibling species which diverged in the Pleistocene. A recent southward dispersal of European R. clavata-like elements along with the W African shelf with the budding of S African R. straeleni is ostensible. The tumultuous Quaternary palaeoclimatic history of equatorial and tropical Africa with the succession of glacial and interglacial palaeoenvironments could have promoted the repeated geographical isolation of local demes in relatively restricted refugial areas. Within the evolutionary trajectories experienced by Rajoidea, structured populations and allopatric sibling species could frequently represent intermediate frames of the microevolutionary animation proposed by Ernst Mayr to model allopatric speciation.