This study explores the genetic diversity and fruit quality parameters of native apple germplasm in the Van Lake Basin, a region characterized by unique apple populations. Combining molecular analysis through Random Amplified Polymorphic DNA (RAPD) and traditional pomological analyses, the research aims to provide a comprehensive understanding of the genetic variability and fruit characteristics of local apple genotypes. In the Van Lake Basin, 137 apple genotypes were evaluated over three years, with 35 promising genotypes selected for further analysis. Genomic DNA was isolated using the CTAB+PVP protocol, and RAPD analysis with ten-mer primers revealed significant genetic diversity among the genotypes. The Jaccard coefficient and UPGMA algorithm were employed for data analysis, resulting in a dendrogram that elucidates the genetic relationships. Pomological analyses encompassed various fruit quality parameters, including fruit weight, volume, flesh firmness, and juice characteristics. Fruit shape indices were categorized, and pH, soluble solids content, and titratable acidity were determined in the fruit juice. Alternate bearing patterns and tree characteristics, such as stem circumference, tree height, and crown width, were evaluated over the three-year study period. The results showcase a diverse array of apple genotypes in the Van Lake Basin, providing valuable insights for germplasm management and conservation. The molecular markers employed in this study contribute to accurate genotype identification, addressing challenges associated with morphological traits. The comprehensive fruit quality assessments offer practical implications for future breeding programs, orchard management, and sustainable apple cultivation in the region. This research serves as a valuable resource for horticulturists, geneticists, and policymakers involved in apple cultivation and conservation efforts. The findings contribute to the broader understanding of local apple genetic resources, emphasizing the importance of integrating molecular techniques with traditional analyses for a holistic approach to germplasm management and breeding strategies.