The methodology used for microscopically examining and enumerating phytoplankton has a major influence on the results obtained. This study describes how counting or not counting picoplankton (cells less than 2 μm) makes a large difference in terms of total abundance and taxonomic composition estimates. We suggest that the type of methodology including the smallest level of detection attempted in terms of size (e.g. macroplankton, net plankton, nannoplankton or picoplankton), should be reported for all phytoplankton studies where organisms are counted. It is also important to restrict data comparisons to studies where the same level of detection is used.