Currently, the distribution of eukaryotic protists is a matter of intense debate. One side of the argument states that because of their small size, protists have the ability to disperse across geographic boundaries. Consequently, geographically structured populations and genetic variation are not expected. The other side argues that some of the bigger protists have limited dispersal and are therefore endemic with limited gene flow. The purpose of this thesis was to investigate the intraspecific genetic diversity of the ciliate ' Carchesium polypinum' (Subclass: Peritrichia) and determine whether that diversity mapped onto the geography of the regions sampled. Sampling was carried out mostly in river basins of Southwestern Ontario, but samples were also obtained from British Columbia, North Carolina, and England. Three nuclear markers - internal transcribed spacer (ITS) 1, ITS2 and the hypervariable region of the large subunit rRNA (28S) - and one mitochondrial gene - cytochrome c oxidase subunit I ('cox-1') - were used for the population-level analyses. This is the first time that the 'cox-1' gene is used on a ciliate other than ' Tetrahymena' and 'Paramecium'. The results indicated that 'C. polypinum' harbors a large degree of genetic diversity; however, in most cases this diversity is not geographically partitioned. This is one of the first times that population genetics analyses are employed on protists. Furthermore, quantitative as well as qualitative analyses, based on both morphological characters and gene sequences of the small subunit rRNA (18S), uncovered robust evidence that 'C. polypinum' is a cryptic species complex with no fewer than six members
