Iron plays an important role in marine primary productivity, and Synechococcus species as major contributors to the total photosynthetic biomass in the world’s oceans might be limited by iron supply in some regions. The present study aimed to compare the photosynthesis and flow cytometric signals of four Synechococcus strains grown under different iron concentrations with either nitrate or ammonium as the sole nitrogen source. Two oceanic strains were much more sensitive to iron limitation than two coastal strains. The inhibition of iron limitation on the growth, maximal PSII photochemical yield, maximal rate of relative electron transport and photochemical quenching of the two oceanic strains was higher than for their coastal counterparts. Under iron limitation condition, the connectivity factor between individual photosynthetic units (ρ) increased for the two coastal strains, while decreased for the two oceanic strains. Furthermore, iron limitation accelerated the Q A re-oxidation of the two oceanic strains and the PQ pool re-oxidation of the two coastal strains. Under iron limitation condition, the cell size of the two coastal strains and intracellular pigment concentrations of the two oceanic strains decreased, while the side light scatter/front light scatter (SS/FS) ratio of the two coastal strains increased. In contrast to iron limitation, nitrogen source only marginally affected the photosynthesis of the four Synechococcus strains. Ammonium enhanced the growth of the two coastal strains under iron-replete condition. For the two oceanic strains, ammonium increased their cell size and decreased their SS/FS ratio and intracellular pigment concentrations under iron-deplete and iron-replete conditions.