The phylogenetic relationships and the geographical origin of 27 of the 34 species and of 3 of the 9 subspecies of Iberian endemic Dytiscidae are studied, based on species level phylogenies constructed with two mitochondrial gene fragments (16S rRNA and Cytochrome Oxidase I). All Iberian endemic species for which more than one specimen was included were monophyletic with the exception of the complex Deronectes aubei sanfilippoi Fery & Brancucci, 1997-D. delarouzei (Jac. Du Val, 1857 (Sharp, 1872) and Hydroporus normandi normandi Régimbart, 1903 do not form well characterised lineages, as measured with the mitochondrial markers used in this study.The Iberian endemic species of Dytiscidae are divided in three groups according to the type of vicariant origin: 1) within-Iberian species, when the sister species (or clade) of the Iberian endemic is also and Iberian endemic; 2) Iberian/European, when the sister occurs in Europe north of the Pyrenees; and 3) Iberian/North African, when the sister occurs in North Africa. Within-Iberian endemics are found to be on average older than Iberian/European and Iberian/North African species, they have more restricted distributions within the Iberian peninsula (they occur typically in only one of the main biogeographical regions), and tend to occur exclusively in running waters. The withinIberian species are best represented by the "Iberian" clade of the genus Deronectes, formed by six endemic species plus two species with wider distributions. Most species in this group originated in rapid succession in the Late Miocene-Early Pliocene boundary by repeated vicariant events in the three main mountain massifs in the Iberian peninsula: the Pyrenees, the Baetic ranges, and the Sistema Central plus mountain massifs of the NW. On the contrary, most of the Iberian/European species seem to be the recent (Pleistocene) vicariants of a species with a widespread distribution encompassing the Iberian peninsula, at present restricted to south and west of the Ebro valley. The results of these analyses suggest that the Iberian peninsula was an isolated refuge during the Quaternary glaciations, in where allopatric speciation was frequent among some lineages of Dytiscidae diving beetles.