Recent studies have documented differences in photosynthetic capabilities between leaves, bracts and the capsule wall of cotton (Gossypium hirsutum L.) but the explanation for this is lacking. Field studies were conducted to related anatomical and physiological parameters associated with carbon fixation to explain the differences in photosynthesis of these three organs. Gas exchange measurements made with a portable photosynthesis systme indicated that the leaves were more photosynthetically active than the capsule wall. Light and electron microscopy of cotton leaves, bracts, and the capsule wall were carried out to elucidate the histological and ultrastructrual differences in relation to their observed photosynthetic activities. Light microscopy revealed that leaf was approximately 152 µm thick, had a well-defined internal palisade mesophyll cells and loosely packed spongy mesophyll cells. In contrast, the bract was thinner (110 µm), lacked a defined palisade layer, and was largely composed of internal air spaces. The capsule wall was very thick (1013 µm) and composed of numerous tightly packed parenchymatous cortical cells with little or no intercellular air space. These observations suggest that the differences in photosynthesis between the leaves, bracts and capsule wall can be explained in terms of anatomical differences associated with the physiological function of gas exchange and carbon fixation. Additional research is necessary to observe whether the photosynthetic enzymes involved behave differently in the bract and the capsule wall in order to further explain the low photosynthetic rates observed.