Sorghum (Sorghum bicolor L. Moench) is a C4 crop species well adapted to stressful environmental conditions. Carotenoids are a group of accessory pigments involved in photosynthesis, photoprotection, and as precursors of absisic acid. A "carotenoid diversity panel" comprised of 87 sorghum lines was assembled to study the association between carotenoid genes and accumulation of pigments in the grain for human consumption. The same panel was used in this study to test the association of 36 markers in these same twelve carotenoid genes (Crtiso, Lcye, Crtrb1, Crtrb2, Zds, Ccd1, Nced3, Lcyb, Crtre, Pds, Psy1 and Psy3) with photosynthesis and photoprotection using Linkage Disequilibrium (LD) mapping. Gas exchange and fluorescence measurements were taken under field conditions in the light and dark in Ames, Iowa, in September 2011, using a LI-COR 6400XT. GLM and MLM analysis revealed that Crtrb1 is associated with qP, Lcye and Crtiso affect Fv/Fm, and Zds is involved in NPQ. The genotypic and phenotypic diversity investigated in this study provides insight into specific reactions in the carotenoid biosynthesis pathway and their role in photosynthesis and photoprotection.