Abstract The “aquatic phycomycetes” constitute an ecologically and economically important assemblage of eukaryotic microorganisms, because they share many morphological traits and important ecological functions and they interact with each other in aquatic ecosystems. The last two decades of research have provided both molecular and structural evidence that the “aquatic phycomycetes” are a diverse, polyphyletic grouping and therefore not a valid taxonomic entity. Very little research has been conducted for many years with the “aquatic phycomycetes”, possibly because in general these microorganisms are often hard to isolate and maintain in most laboratory facilities, little background data has been available to identify the species, the studies were time consuming, the state of the art technology in many cases did not permit studies on these groups and they were thought to be economically and ecologically unimportant. However, this perception has changed recently. For example, some of these species (1) are now known to play important roles in biomass conversion and sequestration of CO2, (2) are parasites of many fungal, plant and animal species, (3) may harbor genes of important enzymes for industrial applications and (4) can serve as indicator species for eco-tox monitoring. This review discusses the assemblages of microorganisms which Sparrow placed into the aquatic phycomycetes, their history in brief and their current phylogenetic placement.