AbstractThe Iberian Peninsula and south‐western France have been postulated as centres of diversification of a wide variety of endemic earthworm species and genera within the Lumbricidae family. However, the phylogenetic position and identity of some of these endemisms is still uncertain and their phylogeographic patterns totally unknown. In the present study, phylogenetic analyses were carried out with the molecular markers COI, 16S, 28S, ND1 and 12S to clarify the phylogenetic position of the Iberian endemism Iberoscolex in the lumbricid tree. In addition, phylogeographic patterns of three of its species (I. albolineatus, I. carpetanus and I. gerardoi) were studied based on the COI marker and compared with patterns of species showing similar distributions within Castellodrilus (C. ibericus and C. chitae), another Iberian endemism. Phylogenetic trees recovered all species of the genus Iberoscolex (with the exception of I. pseudorroseus) within a clade differentiated from Eiseniona where some authors had placed Iberoscolex species before. Moreover, they were clustered with some species (including the type) of Orodrilus, an Iberian‐French endemism also sequenced for this study. Owing to the priority of Orodrilus, Iberoscolex should be considered a junior synonym, with all of the species formerly included within it assigned to a redefined Orodrilus. Strong population structure was observed for Iberoscolex and Castellodrilus species under study, together with a pattern of isolation by distance; however, these genera showed different patterns of genetic variability: the Castellodrilus species under study exhibit lower genetic diversity, with fewer haplotypes per population than the Iberoscolex species.