Microbial parasites typically are characterized by their small size, short generation time, and high rates of reproduction, with a simple life cycle occurring generally within a single host. They are diverse and ubiquitous in aquatic ecosystems, comprising viruses, prokaryotes, and eukaryotes. Recently, environmental 18S rDNA surveys of microbial eukaryotes have unveiled major infecting agents in pelagic systems, consisting primarily of chytrids (Chytridiomycota). Chytrids are external eucarpic parasites that infect diverse prokaryotic and eukaryotic algae, primarily diatoms and filamentous species. They produce specialized rhizoidal systems within host cells, i.e. the nutrient conveying system for the formation of fruit bodies (sporangia) from which propagules (motile uniflagellated zoospores) are released into the environment. In this review, we summarize the ecological potential of parasites of phytoplankton and infer the implications for food web dynamics. We focus on chytrids, together with other parasitic eukaryotes, with special emphasis on (1) the role of microparasites in driving the structure of phytoplankton communities, (2) the role of chytrid zoospores in matter and energy transfer, and (3) the potential consequences of infections for food web dynamics. We raise the question of genetic potential from host -parasite interactions and also of how environmental factors might affect the host -parasite relationships in the pelagic realm.