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This study investigates the variability in the spectral absorption of phytoplankton in Antarctic waters. A large in situ data set comprising phytoplankton pigments and hyperspectral absorption was measured in the northern tip of Antarctic Peninsula during 2013 and 2014 summers at several depths. A proxy of package effect was estimated from the phytoplankton absorption spectra, independently of chlorophyll a. Variations in the concentration of photosynthetic and photoprotective pigments were discernible by changes in this metric but not in the chlorophyll aspecific absorption coefficient of phytoplankton. The fucoxanthin to chlorophyll aratio correlated positively to package effect due to an increase in cell size of phytoplankton (diatoms) and increasing fucoxanthin content per cell to maximize light harvesting in depth. The package effect was found to covary inversely with photoprotective pigments relative to chlorophyll a, partially due to their contribution to enhance absorption in the blue part of the spectrum. Using a cluster analysis (k‐means algorithm) on the phytoplankton absorption spectra, we illustrate the capacity to identify a regular increase in the degree of package effect. This approach can be useful to classify the phytoplankton assemblages in Antarctic waters according to different degrees of pigment packaging, each one related to a specific pigment composition. Our results demonstrate the potential for this classification at different temporal and spatial scales from ocean color satellite data. This should improve our understanding of deviations in global bio‐optical algorithms when applied to the Southern Ocean. Variations in photosynthetic and photoprotective pigments are not discernible by changes in the chlorophyll‐specific absorption of phytoplanktonA cluster analysis identifies a regular increase in the degree of package effect of phytoplankton absorptionA regular increase in the degree of package effect is associated with an increase of fucoxanthin and decrease of photoprotective pigments relative to chlorophyll a