<p>Sour orange (<i>Citrus aurantium</i> L.) is a hybrid species of considerable agronomic, medicinal, and industrial importance; however, its wild genetic resources remain largely underexplored. This study evaluated 24 naturally occurring wild sour orange genotypes collected from the Hassa district of Hatay, Türkiye, using an integrated framework combining morphological, pomological, biochemical, and ISSR molecular markers. The combined use of multi-trait phenotypic measurements and molecular markers enabled a comprehensive assessment of genetic and phenotypic diversity within this localized germplasm. Substantial variation was observed in fruit and leaf traits, indicating strong potential for the selection of contrasting ideotypes. Biochemical analyses revealed marked diversity in total phenolic and flavonoid contents, antioxidant capacity, and vitamin C levels, allowing the identification of genotypes that combine high nutritional quality with commercially acceptable fruit size. ISSR analysis produced a high polymorphism rate (75.72%), confirming pronounced genetic diversity within this micro-region. Multivariate analyses, including correlation, regression, principal component analysis, and hierarchical clustering visualized through heat maps, clearly discriminated genotypes according to fruit size, seed productivity, and phytochemical composition. Overall, the results highlight the presence of considerable genetic diversity within the Hassa district; however, given the geographically restricted sampling, these findings should be interpreted as representative of a localized germplasm rather than the entire species distribution. The study provides a practical basis for selecting superior genotypes for rootstock breeding, fresh fruit utilization, and nutraceutical applications.</p>