Circadian variations of pigment content in the diatom Phaeodactylum tricornutum were analyzed in different light regimes. The study was aimed at discerning the role of putative endogenous controls from the constraint imposed by the alternation of light (L) and dark (D) periods. Our experiments showed that in a typical LD cycle of illumination, pigment synthesis follows the somatic growth of the cell, both arresting during D periods. In particular, the diurnal increase of chlorophyll a content was proportional to the increase in cell size and preceding cell division, occurring at night. By contrast, diadinoxanthin and β– carotene displayed different phases, which is likely to be related to their involvement in photoprotection mechanisms. The experiments also showed that the synthesis of both photosynthetic and photoprotective pigments was dependent not only on light availability and the phasing of somatic growth, but also responded to other internal regulation. Over the time scale of the experiments (hours to days), the removal of LD–DL triggers impaired cell physiology, whereas the circadian patterns in pigment synthesis persisted. Our results support the hypothesis that an internal regulation of cell biosynthetic machinery can improve phytoplankton fitness, even in high variable environments such as the oceanic mixed layers. Therefore, we suggest that phytoplankton growth depends not only on the availability of external resources, but also on internal regulatory mechanisms whose unveiling would further our understanding of phytoplankton diversity and dynamics.