The generalized use of nuclear introns in combination with mitochondrial DNA data in molecular systematic and intraspecific phylogeographical studies is providing new insights into the complex evolutionary histories of taxa surviving the Quaternary glaciations. Previous studies have highlighted the suitability of the beta-fibrinogen intron 7 (β-fibint7) for phylogenetic and phylogeographic studies in a wide variety of taxa, including amphibians. Here we use sequences of this marker to assess inter- and intraspecific variation in Discoglossus (Discoglossidae), with special emphasis on geographic patterns of genetic structure in the Iberian Peninsula, where recent studies have questioned the taxonomic status of D. jeanneae. We obtained 81 sequences of β-fibint7 from samples including all currently recognized species except D. montalentii and 37 populations in the Iberian Peninsula and compared levels of genetic variation with those observed in a fragment of similar length of the mtDNA gene cytochrome b. The sequence of β-fibint7 in Discoglossus is the shortest described for amphibians so far, 378 base pairs. In general, we found low levels of variability (only 26 parsimony-informative sites in the dataset), with no alternatively fixed haplotypes in samples attributed to D. galganoi or D. jeanneae based on their mtDNA. Values of pairwise sequence divergence between non-Iberian species ranged from 1.1% to 4.5% (13.3% to 20.9% in mtDNA). The patterns observed in samples from the Iberian Peninsula are consistent with either incomplete lineage sorting or ongoing gene flow between D. galganoi and D. jeanneae. We conclude by reviewing the genetic evidence available to address the taxonomic status of Iberian species of Discoglossus.