The behaviour of phytoplankton having different abilities to assimilate N in darkness was considered in simulations of vertical migrations. Such behaviour is especially important for the competitive advantage of flagellates, including harmful algal species. Three phases of biomass development were apparent. (1) Cells remained at a subsurface location with migration down to avoid photoinhibitory light at midday; as the attenuation of light increased with biomass growth, the mean depth became shallower. (2) On exhaustion of nutrients in surface waters, cells migrated down through the nutricline in the latter half of the daylight period, with a subsurface maximum in the photic zone as long as light penetration matched requirements. When that condition was no longer met (3), cells migrated between the very surface (forming dense aggregations) and the nutricline. While the ability to perform dark N-assimilation is not critical when N-sources are available at low concentrations, it is important when (as encountered following migration down to a nutricline), nutrients are available at higher concentration in darkness. The most advantageous configuration tested, where nitrate assimilation (as well as that of ammonium) continued at a high rate in darkness as long as C-reserves remained, is not actually used in migratory species but in non-migratory diatoms. The use of the outwardly inferior configurations typical of migratory species, in which dark nitrate-assimilation is notably poorer than assimilation in the light, reflects a deficient metabolism or indicates that N-sources other than nitrate are more important. It is unfortunate then that most attention has been paid to nitrate nutrition in experiments on migrating species. While an ability to continue N-assimilation in darkness as well as during daylight is advantageous, there is no evidence for phytoplankton to be able to grow at high growth rates when decoupling photosynthesis at the surface and N-assimilation at depth.