Synechococcus and Prochlorococcus are among the most abundant photosynthetic organisms on the planet; viruses infecting cyanobacteria (cyanophages) can alter cyanobacterial populations, and therefore affect the local food web and global biochemical cycles. Viruses carry auxiliary metabolic genes (AMGs), which rewire various metabolic pathways in the infected host cell, resulting in increased phage fitness. Coping with stress resulting from photodamage appears to be a central necessity of cyanophages, yet the overall mechanism is poorly understood. In this work, we found novel, widespread cyanophage encoded fatty acid desaturases, capable of modulating the fluidity of the host’s membrane, a fundamental stress response in living cells. We show that both viral fatty acid desaturases (vFADs) families are Δ9 desaturases, catalyzing the desaturation at carbon 9 in C16 fatty acid chains. In addition, we present the first fatty acid profiling for marine cyanobacteria, which suggests a unique desaturation pathway of short fatty acids, in accordance to the vFADs activity. Our findings suggest that cyanophages might fiddle with the infected host’s cell, leading to increased photoprotection and potentially enhancing the viral-encoded photosynthetic proteins, resulting in a new viral metabolic network.