Cultivation of edible mushrooms is the premier agricultural application of mycology. The use of natural biodiversity and molecular genetics for breeding might contribute significantly to the successful outcome of several challenges concerning the management of fruiting induction, fungal diseases, or food quality which growers and mushroom industry participants are faced with. This chapter deals mainly with the saprophytic edible mushrooms belonging to the genus Agaricus, and highlights the button mushroom Agaricus bisporus. The importance of wild germplasm in Agaricus breeding is discussed by stressing the interest of phylogeny for identifying new interesting species or varieties, and the lack of diversity in the cultivated strains, whereas a genetic and phenotypical diversity is now available in Agaricus collections. Breeding strategies adapted to their life cycles and using molecular markers and quantitative genetics are proposed for genetic improvement of Agaricus strains in the era of genomics.