Background: Interactions across the Pyreneans during the Middle-Neolithic (V-IV millennium BCE) have been described for a long time. Nevertheless, except for a few examples and attempts to describe it, the biological impact of these interactions on the human groups' make-up is not yet understood. The present work analyses the biological affinities of different groups from both sides of these mountains that represent the Populations of the Middle-and Late-Neolithic by means of the dental morphology. Methods: We present novel dental morphological data of 221 individuals from 11 archaeological sites. These data have been analysed and compared to those from previously published 20 Iberian sites and one French site. Data were recovered following the ASUDAS protocol, and MMD biological measure was calculated between groups. Results: Our results suggest that there were some differences between the analysed populations. These differences are observed at each side of the Pyrenees, but also across them. Concretely, the coastal groups across the mountains show more affinities between each other than the inland groups. In addition, the differences between groups decrease by the end of the Neolithic. Conclusions: Therefore, our results indicate that the intense trade activities registered in the coastal area between both sides of the Pyrenees would have had the greatest biological impacts in the homogenisation of the groups. Although less intense, the across mountain network and coastal to mountain area trade networks to the south of Pyreneans, also influenced the biological make-up of the groups.