The light absorption properties of phytoplankton (aph(λ)) and non-algal particles (anap(λ)) associated with phytoplankton pigments were analyzed across the Red Sea, in the upper 200 m depth, between October 2014 and August 2016. The contribution by non-algal particles to the total particulate light absorption (aph(λ)+ anap(λ)) was highly variable (23 ± 17% at 440 nm) and no relationship between anap(440) and chlorophyll a concentration, [TChl a], was observed. Phytoplankton specific phytoplankton absorption coefficients at 440 and 676 nm for a given [TChl a], aph*(440) and aph*(676), were slightly higher than those derived from average relationships for open ocean waters within the surface layer as well as along the water column. Variations in the concentration of photosynthetic and photoprotective pigments were noticeable by changes in phytoplankton community size structure as well as in aph*(λ). This study revealed that a higher proportion of picophytoplankton and an increase in photoprotective pigments (mainly driven by zeaxanthin) tended to be responsible for the higher aph*(λ) values found in the Red Sea as compared to other oligotrophic regions with similar [TChl a]. Understanding this variability across the Red Sea may help improve the accuracy of biogeochemical parameters, such as [TChl a], derived from in situ measurements and ocean color remote sensing at a regional scale.