Microzooplankton assemblages in the sea are often dominated by oligotrich and choretrich ciliates. Ciliate communities are diverse and dynamic, with rapid changes in abundance and species composition over short time scales. Understanding the nature and implications of diversity in ciliate communities is critical if we are to extrapolate measurements (e.g. grazing, growth) obtained with one ciliate community or a few species in culture to regional or global models of food webs. In addition, the degree of inter- and intraspecific genetic variability across spatial and temporal scales is unknown for these ciliates. Finally, analysis of morphological markers alone has generated considerable debate between researchers who argue that all ciliates are cosmopolitan versus those who believe that there is limited gene flow between geographically isolated ciliate populations. One key to addressing all of these issues is to quantify the correspondence between molecular markers and morphology within and between populations. At present, however, molecular data are sparse for these ecologically important groups. This project combines molecular and morphological methods to elucidate the diversity of marine ciliates in the subclasses Choreotrichia and Oligotrichia (Cl: Spirotrichea). This large group of planktonic grazers comprises an important trophic link between phytoplankton and bacterial production and higher consumers. The main focus of the study is to collect DNA sequence data from natural populations of choreotrichs and oligotrichs, and to relate these sequences to morphospecies determined by traditional methods. A combination of techniques will be applied to handpicked cells from natural assemblages to evaluate diversity across a range of scales from meters to thousands of kilometers, with intensive sampling of ciliates along the southern coast of New England and the western coast of the United Kingdom. Intraspecific genetic variability will also be quantified as changes within populations over short temporal and spatial scales. The study has two objectives: 1) to quantify diversity within a subset of marine oligotrich and choreotrich species sampled from nearshore environments using both morphology and molecular markers, and 2) to assess patterns of intraspecific variation on short spatial and temporal scales in a few abundant species of oligotrich and choreotrich ciliates. For both objectives, individual cells will be picked for genetic analysis and preserved for species identification. For objective one, small subunit ribosomal gene sequences will be compared. For the second objective, more variable markers will be analyzed, including the internally transcribed spacer regions (ITS1 and ITS2) of the ribosomal genes and an intervening sequence between histones H3 and H4 (H3H4IS). Combining molecular and morphological approaches, this study will produce comprehensive data on genetic diversity of populations of oligotrichs and choreotrichs. These data are an essential first step for connecting information on individual species abundances sampled across time and space to whole communities of ciliates. In addition, this work will provide the first test using molecular data on marine ciliate endemism and will train graduate students in relevant morphological and molecular techniques. The resulting data will have broader implications for questions regarding global protist diversity and biogeography and will be necessary to fully explore the role of ciliates in energy flow and nutrient cycling in marine systems.