The effects of Fe deficiency on the marine cyanobacterium Synechococcus sp. were examined in batch cultures grown on nitrate or ammonium as a sole nitrogen source under two different irradiances. Fe-stressed cells showed lower chlorophyll a content and cellular C and N quotas. Light limitation increased the critical iron concentration below which both suppression of growth rate and changes in cellular composition were observed. At a limiting irradiance (26 μmol.m−2.s−1), this critical value was ∼10 nM, a 10 times increase compared to high-light cultures. Moreover, at low light the cellular chlorophyll a concentration was higher than at saturating light (110 μmol.m−2.s−1), this difference being most pronounced under Fe-stressed conditions. Cells grown on ammonium showed a lower half-saturation constant for Fe (Ks) compared to cells grown on nitrate, indicating Synechococcus sp. has the ability to grow faster on ammonium than on nitrate in a low Fe environment at high light. Consequently, in high-nutrient and low-chlorophyll regions where Fe limits new production, cyanobacteria most likely grow on regenerated ammonium, which requires less energy for assimilation. The Ks for growth on Fe at low light was significantly higher than at high light compared with the cells grown on the same N source, suggesting the cells require more Fe at low light. Therefore, if cells that are already Fe-limited also become light-limited, their iron stress level will increase even more. For cyanobacteria this is the first report of a study combining the interactions of Fe limitation, light limitation, and nitrogen source (NO3− vs. NH4+).