Analysis of quantitative and qualitative composition of rare phytoplankton species was performed using a data set collected over a large geographic area (four eutrophic gulfs of the Aegean Sea, E. Mediterranean Sea) during 2002–2003. We examined the effects of excluding rare species on comparisons of species richness, diversity, similarity and niche breadth as well as the regional and seasonal contribution of rare species to cell abundance and carbon biomass. Overall, the total of 401 species included 182 rare species contributing 45.1% of the total species number. However, there was a considerable variation in this relationship among the other parameters, as rare species contributed only 6.4% of total cell abundance, 13.1% of total species diversity, 21.2% of total cell biovolume and 16.6% of total carbon biomass. The results showed that rarity may be a significant issue in studies detecting and quantifying phytoplankton community structure.