Microscale (decimetre) vertical heterogeneity in the distribution of nano- and microplankton was studied on August 23, 1999 at two different sites (separated by ∼40 m) in Aarhus Bay, Denmark. At the time of sampling, the water column was stratified with respect to both temperature and salinity and a subsurface fluorescence maximum (corresponding to ∼10 μg chlorophyll a l -1 ) occurred immediately below the primary pycnocline (9 m). Samples for species identification were taken at the surface, near the bottom of the water column and at 20 15-cm intervals in and around the depth of maximum fluorescence. The plankton communities recorded in the three different regions of the water column dared dramatically from one another. In addition, significant differences were found in the distribution patterns of species and functional groups in the region of sampling around the fluorescence peak. The same patterns in vertical species distributions were observed at the two stations. In the region surrounding the subsurface fluorescence peak, diatoms were, generally, regularly distributed, although the total diatom biomass decreased slightly with depth. Dinoflagellate species were mainly non-regularly distributed and could be divided into two groups: (i) autotrophic or potentially mixotrophic species (Dinophysis norvegica, Dinophysis acuminata, Dinophysis cf. dens, Prorocentrum micans, Gymnodinium chloiophorum and Ceratium macroceros) that mainly decreased in numbers with depth or were aggregated in their distribution; and (ii) heterotrophic or potentially mixotrophic species (Ceratium lineatum, Ceratium longipes, Ceratium furca, Ceratium tripos, Ceratium fusus, Protoperidinium curtipes, Protoperidinium steinii, Diplopsalis spp. and Katodinium glaucum). In the latter group, the species mainly increased in numbers with depth or were randomly distributed. Most ciliates were uniformly distributed vertically in the water column. However, small cells of the photosynthesizing ciliate Mesodinium rubrum were most abundant at the depth of maximal fluorescence while large M. rubrum cells were equally abundant at all the depths sampled, suggesting the two size groups of this organism may differ ecologically. Overall, the study demonstrates that traditional plankton sampling methods may lead to misinterpretations of species co-existence and interactions.