We have studied in this work the natural variability in Holm oak (Quercus ilex subsp. ballota) by analyzing acorn morphometry and chemical composition in 13 populations from the Andalusia region (southern Spain). Acorn morphometry showed statistic significant differences between the populations with a higher acorn weight, length, and diameter in the northern provenances (TJA, GSE, CTH, CHU, APS, and PCO), while the Southern provenances (RMA, SAA, CCO, BCA, and SCA) showed lower value that even decreased with the altitude. Acorn chemical composition also showed statistic significant differences between populations. Morphometry and chemical composition data were subjected to clustering analysis, and two major clusters were detected. This analysis showed that northern populations (CTH, TJA, SCA, CHU, PCO, GSE, and APS) showed a tendency to present values highest in acorn weight (5.42 g vs. 3.21 g); acorn length (37.21 mm vs. 28.73 mm); acorn diameter (16.12 mm vs. 13.79 mm); ash (1.88% vs. 1.55%); protein (4.82% vs. 4.38%); fat (12.55% vs. 9.92%); and oleic acid (66.93 vs. 66.4%). On the contrary, Southern populations (SSA, VJA, CCO, BCA, RG, and RMA) showed a tendency to present values lowest in sugar (10.28% vs. 11.25%); energy (20,076.71 kJ/kg vs. 20,149.26 kJ/kg); palmitic (16.11% vs. 16.39%) and linoleic acids (13.07% vs. 13.11%). The populations studied here seemed to integrate acorn morphology and chemical composition related to environmental conditions of the original provenances. These data have provided biochemical markers that help establish phylogenic associations between populations and also reveal potentially account as an alternative source for dietary nutrition.