Mentzelia monoensis J. M. Brokaw & L. Hufford is a cryptic hexaploid species known only from Mono County, California. Previous studies have suggested a recent allopolyploid origin of M. monoensis but have not investigated the causes of its narrow distribution. Here we report the discovery of a unique haplotype from the chloroplast intergenic spacer ndhF-rpl32 that is sufficient to distinguish M. monoensis from all other species in Mentzelia sect. Trachyphytum using preserved specimens from any developmental stage. Based on soils collected with verified voucher specimens, we show that the edaphic niche of M. monoensis is significantly different from those of all other species in Mentzelia sect. Trachyphytum. A principal components analysis suggests the edaphic niche of M. monoensis is also one of the most extreme in Mentzelia sect. Trachyphytum. Most populations of M. monoensis were collected in soils derived from silica-rich rhyolite tephra produced by the Mono Craters volcanic chain. These coarse textured soils are lower in cation exchange capacity and plant available nutrients than those of any other species in Trachyphytum. Our findings suggest that edaphic specialization may have played a significant role in the establishment and geographic distribution of M. monoensis and other species in the Mono Basin.