The question of what limits primary productivity and phytoplankton biomass in natural waters has occupied oceanographers and limnologists for more than a century. To a large extent the difficulty in determining what limits primary production stems both from methodological deficiencies and semantic confusion. The identification of limiting factors has been based on primarily three techniques: correlative inference, experimental manipulation, and simulation modeling. Here the authors examine the concepts of limiting factors and explore the possibility of using in vivo chlorophyll fluorescence (a biophysical signal), in conjunction with molecular markers, to identify or diagnose factors limiting phytoplankton growth and production in the ocean.