The question of whether one large, continuous area or many smaller habitats maintain more species is one of the most relevant questions in conservation ecology, and it is referred to as the SLOSS (Single Large Or Several Small) dilemma in the literature. This question has not yet been raised in the case of microscopic organisms, therefore we investigated whether or not the SLOSS dilemma could apply to phytoplankton and benthic diatom metacommunities. Benthic diatom and phytoplankton diversity in pools and ponds of different sizes (ranging between 10-2-107 m2) was studied. Species richness of water bodies belonging to neighbouring size categories was compared step by step across the whole size gradient. With the exception of the 104-105 m2 and 105-106 m2 size categories, where phytoplankton and benthic diatom richness values of the SL water bodies were higher than that of the SS ones, findings showed that the diversity of several smaller (SS) sized waters was higher than that in single large water bodies (SL) throughout the whole studied size range. The proportion of the various functional groups of algae, including both the benthic diatoms and phytoplankton, showed remarkable changes from the smaller water bodies to large sized ones.