Satellite ocean color data enable the global assessment of the ocean biosphere through determinations of chlorophyll concentrations. However, ocean color is not a function of chlorophyll alone. We assess differences between two ocean color models with nearly identical validation statistics. The resulting chlorophyll retrievals show systematic differences which are consistent with each model's ability to account for the absorption of light by colored dissolved organic materials. These differences are often large and approach 100% poleward of 40° latitude. We conclude that the discrepancies are due to fundamental differences in model assumptions and their empirical tuning using geographically limited, in situ data. This source of uncertainty is important as the choice of ocean color model alters modeled rates of global net primary production by more than 30%. The ultimate resolution of this issue requires continued improvements in remote sensing algorithms and validation data as well as satellite technology.