Background <p>Hot pepper (<i>Capsicum spp.</i>) is a vital crop for both agricultural sustainability and traditional food systems in Southeastern Türkiye. However, increasing exposure to prolonged heat and seasonal drought poses serious threats to yield stability, fruit quality, and genetic diversity. To support climate-resilient breeding, this study evaluated the genetic structure and agro-morphological diversity of 60 selfed (S3-stage) genotypes derived from Gaziantep landraces. These genotypes were developed through single-plant selection and selfing over three generations (2018–2023), and tested under natural field-based heat stress conditions.</p> Methods and results <p>Twenty agro-morphological traits were recorded using UPOV TG/76/8 descriptors. Molecular profiling employed 30 polymorphic markers (12 ISSR, 10 SRAP, and 8 SSR). STRUCTURE, DAPC, and UPGMA analyses consistently revealed three distinct genetic clusters (K = 3), supported by ΔK and BIC criteria. AMOVA showed that 81% of the total genetic variation occurred within groups and 19% among groups (Φ_PT&#xa0;= 0.192, <i>p</i> &lt; 0.001). A Mantel test confirmed a moderate yet significant correlation (<i>r</i> = 0.411, <i>p</i> = 0.002) between molecular and morphological distances. Genotypes G53 and G58 exhibited strong allelic divergence along with superior field performance, indicating their potential for marker-assisted selection under heat stress.</p> Conclusions <p>This study demonstrates the presence of structured genetic diversity and adaptive potential among S3-stabilized <i>Capsicum</i> genotypes. The combined use of multilocus genotyping and field-based phenotyping under real-world abiotic stress offers a replicable framework for identifying elite lines. These findings contribute to the development of climate-resilient pepper cultivars suited to semi-arid and Mediterranean agroecological regions.</p>