In order to study the genetic control of sunflower fatty acids under optimum and water limited conditions a set of 12 sunflower hybrids were evaluated as randomized complete block design with three replications in two separate experiments during two years (2019 and 2020) in Karaj Iran. The hybrids were obtained by crossing of four male sterile lines and three restorer lines as testers. Water limitation was imposed by water withholding during reproductive stage. Palmitic acid content was governed by both additive and non-additive effects and linoleic acid content by non-additive gene action under optimum and water limited conditions. Stearic acid content was controlled by both additive and non-additive effects in optimum but by additive effects under water limited condition. Oleic acid content was governed by non-additive factors in optimum while by both additive and non-additive effects in water limited condition. Oil content and leaf temperature were inherited by additive and seed yield by additive and non-additive effects in both conditions. Relative water content and chlorophyll content were controlled by both additive and non-additive effects under optimum but by non-additive effects in water limited condition. According to these results hybrid breeding is suggested for improvement of main sunflower fatty acids under optimum and water limited condition except that selection-based methods for improvement of stearic acid content.