The study focused on assessing the genetic basis of photo and drought stress in the Persian walnut, an important cultivated nut crop. Genome-wide association analysis and pathway enrichment provided insights into the photosynthetic responses to drought stress in Persian walnut. This research provides a foundation for future walnut breeding programs focused on improving drought tolerance and suggests the potential of natural photosynthetic variation in walnuts as a valuable resource for breeding and engineering more efficient photosynthesis.