We conducted habitat, germination, and population genetic studies to inform management priorities for Phacelia cookei Constance & Heckard (Boraginaceae), a diminutive annual herb known from only four populations near Mt. Shasta in Siskiyou Co., California. Habitat surveys characterized soil, vegetation, and ground cover of extant populations and attempted to identify potentially suitable, but uncolonized, habitat. We were unable to distinguish any sites based on tests of soil characteristics. Nama densum Lemmon occurred at all sites where P. cookei was present. We identified several areas near existing populations that appeared to be suitable, but uncolonized, habitat. We tested the effects of various factorial combinations of after-ripening, scarification, stratification, and variable germination temperatures on breaking seed dormancy. Seed viability by tetrazolium tests ranged between 89% and 93%, but the highest germination from any treatment combination was 14% after adjusting for seed viability. We resolved 19 putative allozyme loci, two of which were polymorphic. Apparent genetic diversity was low both within and among the three sampled populations compared to similar endemic species, and populations were genetically similar. Management plans could consider attempting to expand existing populations by sowing seeds from existing populations into similar habitat.