The recurrent detection of parasitic zoospores among aquatic heterotrophic flagellates has recently changed our view of how the microbial loop is organized, and has called into question the role of eukaryotic parasites in the aquatic 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 molecular methods (sequencing of clones libraries). In marine systems, this group is known to comprise only 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. Recently, we designed specific oligonucleotidic probes to target Perkinsozoa in order to quantify them and estimate its in situ dynamics in lacustrine systems. The first quantitative results obtained through a monthly sampling (annual survey) confirmed the quantitative importance of Perkinsozoa free-living stages in lakes, especially during summer in the epilimnion (Mangot et al, 2009 ; Lepère et al, 2010). We investigated, in this study, the short-term variations of the Perkinsozoa abundance (zoosporic stage) using TSA-FISH in the mesotrophic Lake Geneva in summer 2009. From this approach, a new host-parasite association could be observed between a Chlorophyceae specie (Volvocales) and a member of the Perkinsozoa phylum. Isolation of infected hosts, combined with molecular analysis (genome amplification) of these single cells should reveal the phylogenetic identity of the host and the lacustrine perkinsids.