Background Stone pine (Pinus pineaL.) is harvested for its edible kernels. It is an important forest tree species, and also plays an important role in afforestation. Successful afforestation activities strongly depend on the quality of seeds and seedlings. Five eastern native populations of stone pine were analyzed, in terms of their geographical and climatic parameters, in order to identify their cone, seed, pine nut, and seedling traits. With this regard, we aimed to contribute to the reforestation, yield, and breeding of this species. Results All native populations occur in the sub-humid bioclimatic zone, according to Emberger's bioclimatic classification, ranging 74.7-63.2 of Emberger'sQIndex value (Q), which synthesizes humidity and temperature, with lower values indicating more arid conditions. With regard to geographical factors, altitude was found to have the greatest effect on cone diameter and seed weight, while there was a weak correlation of cone, seed, and pine nut dimension with longitude and latitude. In terms of climatic factors,Qand mean of the maximum temperature of June, July, and August (ME) were found to be the main drivers behind significant effects in cone, seed, and pine nut morphometric traits. The most negative effect on seed number cone(-1)(r: - 0.897), pine nut number cone(-1)(r: - 0.923), pine nut yield (r: - 0.903), and pine nut weight (r: - 0.878) wasQ, whereas cone diameter, seed length, and seed weight were positively correlated with the ME (r: 0.939,r: 0.889, andr: 0.866, respectively). Cone and seed diameter and seed weight increased with decreasing summer drought index (r: - 0.806,r: - 0.846, andr: - 0.866, respectively). Rainfall in the June of the third year prior to harvest time (RJ) had a negative effect on the percentage of sound seeds per cone. Annual rainfall in the third year prior to harvest time (AR) significantly affected pine nut weight (r: 0.889), although rainfall during summer had a negative effect. The empty seed ratio of the different populations ranged from 20 to 68%, while considering all populations, the empty seed ratio was 46%. Conclusions The study suggests that theQIndex and ME should be taken into account to determine cone to pine nut yield. With this regard, plantations of stone pine should be established on sub-humid areas andQvalues should not exceed 75.