The objectives of the present research were to evaluate the variability induced by gamma-irradiation among a population of M8 sunflower mutant lines and to identify molecular markers associated with different seed germination traits. Experiments were carried out under well watered and water-stressed conditions using a randomized blocks design, with three replications. The studied traits consisted of critical times (the time to starting germination, TSG), the time to 50% germination (T50%G) and the time to maximum germination (TMG) and the percentage of seed germination (PSG). In both conditions, a large genetic variation was observed among mutant lines. Some mutant lines showed higher values of germination parameters when compared with the original lines (AS613). Results revealed the a efficiency of gamma irradiation for inducing genetic variation in sunflower, for germination traits. A highly negative, significant correlation was observed between PSG and the critical times of germination. Mutant line “M6-39-2-1” was significantly superior to the original line, for the studied traits, under the water-stressed condition. Multiple regression analyses showed that some AFLP markers were associated with several traits. The most informative AFLP markers were “E37M62-5” and “E33M60-6” which did not have any interactions with water stress. Several markers were associated with seed germination parameters in both conditions. The markers which were associated with different traits could be used in marker-assisted selection for germination parameters.