The common gudgeon Gobio gobio (L.) has a great phenotypic plasticity being one of the most variable fish species in Europe. In the Iberian Peninsula it has been considered to be an introduced species. However, recent publications have considered that gudgeon populations from different basins of the Iberian Peninsula are native. in this work we tried to clarify the status of Iberian populations by means of molecular methods. thirty-two specimens of common gudgeon from several localities placed in six different Iberian and South French basins (Duero, Ebro, Tajo, Nansa, Bidasoa and Nivelle) were analysed. We reconstructed the phylogenetic relationships between the Iberian gudgeon populations using the whole cytochrome b gene sequence (1141 bp). Moreover, one specimen of G. gobio from the Danube basin and two specimens of Ramanogobio (R. ciscaucasicus and R. uranoscopus) were also included in the study. Our data confirmed the monophyly of the Iberian-French populations analysed and indicated a high genetic differentiation with respect to the common gudgeon populations from Central Europe. However, our results also indicated a very close genetic relationship among the populations of different Iberian basins, showing low genetic distances between them. The absence of population structure among the Iberian populations of G. gobio seems to be due to human activity.