Selenium-enriched yeast (selenium yeast) are one of the most popular sources of selenium supplementation used in the agriculture and human nutritional supplements industries. To enhance the production efficiency of selenium yeast, we sought to develop a method to identify, and ultimately select for, strains of yeast with enhanced selenium accumulation capabilities. Selenite resistance of four genetically diverse strains of Saccharomyces cerevisiae was assayed in various conditions, including varying carbon sources, nitrogen sources, and phosphate amounts, and they were correlated with selenium accumulation in a commercially relevant selenium-containing growth medium. Glycerol- and selenite-containing media was used to select for six yeast isolates with enhanced selenite resistance. One isolate was found to accumulate 10-fold greater selenium (0.13 to 1.4 mg Se g−1 yeast) than its parental strain. Glycerol- and selenium-containing medium can be used to select for strains of yeast with enhanced selenium accumulation capability. The methods identified can lead to isolation of industrial yeast strains with enhanced selenium accumulation capabilities that can result in greater cost efficiency of selenium yeast production. Additionally, the selection method does not involve the construction of transgenic yeast, and thus produces yeasts suitable for use in human food and nutrient supplements.