Geothermal springs, commonly called hot springs, are ubiquitous features of volcanic habitats. Solfatara areas with low pH high temperature flowing hot springs present model environments for studying processes underlying extremophile microbial diversity. Archaea have been isolated and found to thrive under these extreme conditions, yet difficulties in recovering suitably pure environmental DNA persist. Studies have attempted to discover archaeal diversity from volcanic environments, but the presence of heavy metals, low pH, inhibitory substances, and sediment adsorption complicate DNA isolation and diversity studies, particularly of Archaea commonly found in these extreme conditions. In this study, we used a carefully designed comparative analysis of acidic thermal springs of Yellowstone National Park to determine how abiotic factors (chemistry and temperature) structure archaeal communities. Environmental sites of comparable pH were classified by X-ray microanalysis of sediments as sulfur, iron, and iron over sulfur; electronic probes were used to measure the pH, temperature and Eh (reduction potential) of the spring waters.16S rRNA gene sequences were PCR amplified for archaeal DNA, cloned and sequenced, using evolutionarily conserved universal and archaea-specific primers with environmental DNA extracted from Amphitheater Springs and Roaring Mountain sediment samples. Although, we were not able to extract archaeal DNA from all of the sites sampled, demonstrating the difficulty of environmental DNA extraction. Microscopic analysis of sediments by DAPI, SEM, and TEM found the presence of Archaea only in the highest temperature of each sample site, signifying Archaea prefer to live at temperature extremes. Phylogenetic analysis found exceptionally strong correlations between archaeal diversity and sediment mineral chemistry. For example, sulfur-rich sediments contained a high diversity of Crenarchaeota, while iron-rich sediments were dominated by Euryarchaeota. Also, a detailed microscopic analysis found a unique new structure of archaeal flagella in one of the springs, AS102 sulfur spring.