A seed zone or provenance region is an area within which plants can be moved with little risk of maladaptation because of the low environmental variation. Delineation of seed zones is of great importance for commercial plantations and reforestation and restoration programs. In this study, we used AFLP markers associated with environmental variation for locating and delimiting seed zones for two widespread and economically important Mexican pine species (Pinus arizonica Engelm. and P. durangensis Martínez), both based on recent climate conditions and under a predicted climate scenario for 2030 (Representative Concentration Pathway of ~4.5 Wm−2). We expected to observe: (i) associations between seed zones and local climate, soil and geographical factors, and (ii) a meaning latitudinal shift of seed zones, along with a contraction of species distributions for the period 1990–2030 in a northward direction. Some AFLP outliers were significantly associated with spring and winter precipitation, and with phosphorus concentration in the soil. According to the scenario for 2030, the estimated species and seed zone distributions will change both in size and position. Our modeling of seed zones could contribute to reducing the probabilities of maladaptation of future reforestations and plantations with the pine species studied.