An overview of the pigment composition and bio-optical characteristics (spectral light absorption and fluorescence properties) in important marine phytoplankton (diatoms, dinoflagellates, prymnesiophytes, prasinophytes, chlorophytes, euglenophytes, chrysophytes, raphidophytes, cryptophytes and cyanobacteria) are presented. The species/classspecific and photoacclimative characteristics of different pigment groups of phytoplankton are discussed with respect to their pigment composition and their corresponding in vivo bio-optical characteristics. Group-specific differences in pigment-protein (light harvesting complexes and photosystem I and II) composition, abundance and function, together with the package effect (intracellular self shading) which are important variables when interpreting bio-optical information, are discussed. A scaling procedure for photosystem II related in vivo fluorescence excitation spectra is also discussed.