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Abstract The genus Crataegus (Rosaceae) exhibits remarkable taxonomic diversity in Iran, with seventeen recognized taxa distributed across contrasting ecological zones. In recent years, hawthorn has gained prominence as a valuable botanical resource, with applications spanning both herbal medicine and functional food development. Historically, various plant organs, particularly fruits, leaves, and flowers, have been employed in traditional remedies targeting cardiovascular disorders, including hypertension, arrhythmias, and other cardiac complications. These therapeutic properties are primarily attributed to the rich array of secondary metabolites characteristic of hawthorn, notably phenolic compounds and anthocyanin pigments, which underlie its antispasmodic and analgesic effects. We investigated the morphological, biochemical, and phytochemical diversity of eight Iranian Crataegus pontica ecotypes collected from geographically distinct regions. Ecotype origin and environmental conditions significantly influenced all measured parameters ( p < 0.05). Substantial variation was observed in fruit morphometrics, with CPE3 (Miyaneh) and CPE5 (Taleqan) producing the largest fruits, while CPE6 (Sanandaj) and CPE7 (Khorramabad) yielded considerably smaller ones. Biochemical profiling revealed marked ecotypic differences in total soluble solids, soluble carbohydrates, vitamin C, carotenoids, and anthocyanins, reflecting the profound influence of environmental conditions on primary and secondary metabolism. High-altitude ecotypes, particularly CPE3, CPE4 (Alamut), and CPE5, consistently exhibited the highest concentrations of total phenolics, total flavonoids, and antioxidant capacity. HPLC-based phenolic profiling identified chlorogenic acid, hyperoside, rutin, quercetin, and kaempferol as predominant compounds, with ecotype-specific accumulation patterns distinguishing high-antioxidant genotypes such as CPE5, CPE6, and CPE1 (Mahabad). Strong positive correlations among total phenolic content, total flavonoid content, and FRAP values confirmed phenolic compounds as primary determinants of antioxidant potential. Multivariate analyses classified the ecotypes into three functional groups: sugar-rich, large-fruited types (CPE3–CPE4); phenolic- and antioxidant-enriched types (CPE5–CPE6); and intermediate types with moderate metabolite profiles (CPE1, CPE2, CPE7, CPE8). Canonical correspondence analysis revealed altitude, precipitation, and temperature as key environmental drivers shaping phytochemical biosynthesis. We conclude that C. pontica exhibits substantial metabolic plasticity in response to environmental variation, with high-altitude ecotypes demonstrating superior phytochemical profiles as promising candidates for breeding programs and nutraceutical development.