ABSTRACT Peach ( Prunus persica [L.] Batsch) is a vital fruit species in the Rosaceae family, known for its nutritional and commercial importance. Despite its global distribution, modern peach cultivars exhibit limited genetic diversity due to their descent from a few common ancestors. This study assessed the morphological and pomological diversity of 45 native peach accessions from Sistan‐va‐Baluchestan Province, Iran. The evaluation of 46 traits revealed significant phenotypic variability among the accessions. ANOVA showed highly significant differences ( p < 0.05 ) for traits like fruit weight (16.62–32.27 g), fruit flesh thickness (7.14–10.50 mm), and total soluble solids (TSS, 11.3%–20.8%). Tree growth habit had the highest coefficient of variation (70.14%), while fruit flesh percentage showed the lowest (3.64%). Correlation analysis revealed strong positive relationships between fruit weight and fruit flesh percentage ( r = 0.70, p < 0.01), while a trade‐off was observed between fruit flesh percentage and TSS ( r = −0.30, p < 0.05). The first three principal components explained 37.65% of the total variation, capturing key patterns in the dataset. Multiple regression analysis (MRA) revealed that fruit weight was significantly influenced by fruit flesh percentage ( β = 0.91, p < 0.00), stone weight ( β = 0.70, p < 0.00), and petal width ( β = 0.06, p < 0.00). TSS was positively associated with stone diameter ( β = 0.65, p < 0.00) but negatively correlated with fruit weight ( β = −0.38, p < 0.01). Among the studied accessions, the first 15 accessions with the highest scores based on individual quantitative datasets were identified as “Panjebog‐19,” “Panjebog‐26,” “Rachedr‐1,” “Panjebog‐20,” “Panjebog‐2,” “Panjebog‐8,” “Panjebog‐24,” “Panjebog‐30,” “Panjebog‐32,” “Panjebog‐10,” “Panjebog‐3,” “Panjebog‐7,” “Panjebog‐33,” “Rachedr‐5,” and “Panjebog‐27.” This study highlights the significant genetic diversity in the studied accessions, showcasing their value for breeding programs. “Panjebog‐19” and “Panjebog‐20,” being among the top 15 superior accessions and positioned outside the 95% confidence ellipse, show potential for developing high‐yielding and high‐quality peach cultivars. Conservation of local germplasm is crucial to counteract urbanization and agricultural pressures. These findings provide a strong foundation for utilizing genetic resources to address challenges in modern peach production, including limited genetic diversity and changing consumer demands, and to promote sustainable breeding strategies. Future studies should focus on integrating molecular markers with morphological and pomological data to improve the understanding of genetic diversity and to develop more targeted breeding strategies.