Assessing soil biodiversity at the McMurdo (MCM) LTER is an expedient precursor to unraveling ecological interactions in this relatively simple ecosystem. In the McMurdo Dry Valleys (MDV) of Victoria Land, Antarctica, few studies have investigated the diversity of soil ciliates despite their known ecological importance in microbial ecosystems worldwide. Generally, soil ciliates are key bacterial grazers, improving nutrient cycling capacities of bacterial prey by 1) maintaining bacterial populations in the exponential growth phase and 2) mobilizing nutrients to other parts of the food web. Soil ciliates additionally connect larger microscopic predators to bacterial communities by serving themselves as prey (e.g to nematodes and/or tardigrades) As such, they are key in maintaining microbial biodiversity. Because of their ecological proximity to bacteria, they can be considered as first responders to shifts in bacterial communities. This has significance in context of the MDV, where the environment’s hypersensitivity to climate disturbances has major impacts on microfauna community composition and therefore function. However, ciliate diversity in the soils of the MDV is virtually unknown, despite a smattering of morphology-based papers and a portion of a DNA-based study. In light of this, we here present the first steps toward a comprehensive study of soil ciliate diversity and distribution across a few of the major valleys in the MDV system, namely: Wright, Taylor, Garwood, Miers and Hidden. We ask, 1) what the diversity of ciliates is in these valleys, 2) what their relative abundances are and 3) what their ecological roles are (where possible using literature searches). Sequences were obtained through a combined approach of metagenemic and metagenetic sequencing. Ciliate sequences were extracted from the full dataset and identified using MG-RAST, an online metagenomics server and software tool-kit. Using this dataset, we 1) compared the diversity of OTUs recovered in this study with previous morphological assessments; 2) evaluated community composition across samples (and valleys) to identify the most commonly occurring and most abundant species (using OTU percentage as a proxy); 3) estimated the ecological role of the recovered taxa through literature searches. Our results demonstrate that 4 out of 68 total OTUs are shared between all samples, and that there is a potential rich diversity of trophic roles amongst the recovered ciliate taxa, including predators (of other protists), algavores, parasites, and bacterivores. Importantly, recovery methods in this study do not produce results of significant resolution to determine with certainty neither taxonomic nor functional identify of these OTUs. However, the results do suggest that 1) there is a far higher potential diversity present in these soil than previous studies have demonstrated, and 2) that there is room for a complex web of trophic interactions beyond that of bacteria and their grazers.