<p>This is the first study to examine the combined inheritance of hypocotyl pigmentation and ray floret color in the newly developed sunflower mutant PYRS-1 and its implications for breeding efforts. Analysis of F₁ and F₂^s of the reciprocal crosses between two contrasting genotypes, <i>viz.</i>, CMS-1001B (green hypocotyl with yellow ray florets) and PYRS-1 (purple hypocotyl with pale-yellow ray florets) indicated dominant inheritance of purple over green hypocotyl pigmentation and yellow over pale yellow ray florets. Backcrosses with green hypocotyl and pale-yellow ray floret parents consistently exhibited a 1:1 ratio, highlighting the recessive nature of the green hypocotyl and pale-yellow ray floret traits. The joint segregation analysis showed that hypocotyl and ray floret colors are not linked and segregate independently in a 9:3:3:1 ratio. Therefore, these traits could be used individually as morphological markers in genetic studies to determine the genetic purity of F₁ hybrid seeds and estimate the rate of outcrossing in sunflower. To identify molecular markers associated with ray floret color, two SSR primers viz., ORS 812 (LG 15) and ORS 785 (LG 4) out of 56 markers displaying parental polymorphism were able to differentiate the ray floret phenotypes in the F₂ and BC₁ individual samples. The markers ORS 812 and ORS 785 were found to be linked to flower color with PVE of 48.95 and 43.23%, respectively. A QTL (<i>qPY15.1</i>) region associated with pale yellow petal color was mapped between ORS 812 and ORS 8 with a LOD score of 7.01. The study underscores the importance of understanding the inheritance pattern of hypocotyl pigmentation and ray floret color in the sunflower crop, as these traits have implications for breeding goals.</p>