Mushrooms have been attracting attention as a source of bioactive compounds for the development of dietary supplements and medicines. Many researchers have reported pharmacological effects of edible mushrooms, and have isolated and identified bioactive substances. Lentinula edodes (shiitake) and Flammulina velutipes (enokitake) are the cultivated edible mushrooms that are popular throughout the world. In L. edodes, polyacetylenes and sulfur compounds have been shown to display antimicrobial activity. In F. velutipes, many types of bioactive terpenes have been reported from mycelium culture filtrate or solid culture substrate. This article reviews the bioactive metabolites of low-molecular weight from L. edodes and F. velutipes.