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A tectonothermal study of the northeastern sector of the Cantabrian zone (Ponga-Cuera and Picos de Europa units) using the conodont color alteration index (CAI) and Kübler index (KI) methods shows a variation from diagenetic to anchizonal conditions. The latter are illustrated in geological maps and cross sections. The greater part of the studied area has CAI values lower than 2, caused by two long periods of burial separated by a compressive interval (corresponding to the Variscan deformation), in which thrusts were the dominant structures. Tectonic superimposition was balanced by intense and fast erosion and had little effect on the CAI values. In contrast, a high thermal gradient was produced in the southern outcrops that led to recognize the transition between diagenetic and anchizonal conditions through CAI values near the basal thrust of the Picos de Europa unit. The diagenesis/anchizone boundary appears a little further south through the determination of the Kübler index in phyllosilicate minerals (KI = 0.42). CAI isograds cut the Variscan structures as a consequence of a thermal episode that occurred near the Carboniferous–Permian boundary at the beginning of an extensional regime. The thermal source was located further south, in the adjacent Pisuerga-Carrión unit. Alterations in the CAI values, as well as dolomitization and ore deposits, locally resulted from Permian–Mesozoic hydrothermal activity. Microtextural analysis of the conodonts allowed us to relate several types of apatite overgrowth to diagenetic conditions and recrystallization to anchizonal ones, whereas dissolution was common during hydrothermalism. Alpine deformation hardly produced any changes in the previous thermal pattern, but was responsible of the northwards tilting of the structure and CAI isograds. © 2016, Springer-Verlag Berlin Heidelberg.