Heterotrophic protists are abundant and ecologically important members of marine ecosystems. They influence energy flow and biogeochemical cycling by consuming prokaryotes and remineralizing nutrients. They also serve as trophic links between microbial and metazoan food webs. To advance our understanding of microbial community structure and trophic relationships, I aim to characterize the distributions, diversity and trophic dynamics of heterotrophic protists in three different marine ecosystems using a combination of microscopy, molecular and analytical approaches. Using epifluroescence microscopy, I completed the first characterization of seasonal variability in abundance, biomass and size structure of pico- and nano-sized autotrophic and heterotrophic protists at Stn. ALOHA. This study indicates that trophic interactions of protistan grazers impact the structure of lower trophic levels over seasonal and interannual time-scales. The novel application of a method developed for simultaneous determination of rates of viral lysis and grazing mortality in the California Current Ecosystem enabled me to examine the relationships between picoplankton growth and mortality over a range of environmental conditions. The variability in mortality patterns for individual populations and inverse relationship between virus and grazer impacts highlight the complexity of predator-prey interactions in the marine environment. The use of molecular methods in a deep-sea methane seep enabled me to characterize the spatial distribution and diversity of marine protists in response to habitat heterogeneity within seep sediments and provide insights into the environmental factors that structure protistan communities on a range of spatial scales. In addition, the discovery of folliculinid ciliates living in five methane seeps along the Pacific margin is notable because this group of protists is a previously unrecognized, but potentially ecologically important component of seep ecosystems. Using a combination of molecular and analytical tools, I was able to provide the first direct evidence for the incorporation of methane-derived carbon by protists in deep-sea methane seep ecosystems. Characterizing protistan communities and their trophic interactions in response to varying environmental conditions is a key step towards understanding how this group of organisms influences microbial community structure and ecosystem function. The results from these studies highlight the importance of mortality processes, not just variations in growth, for structuring microbial communities. They also demonstrate how continued use and integration of multiple complementary approaches will enhance progress in exploring the underlying mechanisms regulating microbial community structure and trophic dynamics. Such information is critical for accurately predicting the response of microbial communities to a changing environment.