The recurrent detection of parasitic zoospores among aquatic heterotrophic flagellates (HFs) has recently modified our view of how the microbial loop is organized, and called into question the role of eukaryotic parasites in the aquatic trophic food web. The Perkinsozoa group, already known to play a significant role as parasite in marine systems, is of special interest here, since it has recently been detected in several lakes by constructing clone libraries. In marine systems, this group is known to consist solely of intracellular parasites of molluscs or phytoplanktonic species, but their hosts in freshwater environments are still unknown, and little is yet known about their functional importance in planktonic systems. This review summarizes the main information currently available about Perkinsozoa through a description of their phylogenetic position, their life cycles, and regulatory factors, and the consideration of the specificities of their hosts in marine systems, and the few data recently acquired in lakes.