Abstract The origin and distribution of the species of freshwater interstitial (stygobiont) syncarids of the Iberobathynella genus (Crustacea, Parabathynellidae), endemic to the Iberian Peninsula, are considered in the context of evolutionary biogeography. We established the most likely phylogenetic relationships between the 14 known species of the Iberobathynella genus on the basis of morphological characters. We assumed a common marine ancestor and estimated the possible phylogenetic ages of the 14 inland species from the number of cladogram nodes. The land ages at the sites where the species are found help to tell us when the landmasses emerged definitively: most species are found in areas that have undergone one or more marine transgressions/regressions since the Triassic and which could therefore have been colonized by the common ancestors. We assessed the Boutin–Coineau two‐step model of colonization and evolution in an attempt to elucidate the evolutionary history of Iberobathynella and to offer a plausible palaeogeographical scenario. We looked for concordance between the possible chronology of Iberobathynella taxa colonization and their phylogenetic relationships, but found none of significance. Hence, we cannot reject the possibility that evolutionary clade divergence within the genus was independent of sea‐level changes in the Senonian (88.5–65 mya) and Eocene (56.5–35.4 mya) epochs. We can therefore neither confirm nor rule out a correlation.