Two new cuparene-type sesquiterpenes, enokipodins C (1) and D (2), were isolated from culture medium of an edible mushroom, Flammulina velutipes, along with enokipodins A (3) and B (4). The structures of 1 and 2 were determined using spectroscopic methods (HRMS, (1)H and (13)C, and 2D NMR). The absolute configuration of enokipodin C was determined from the observed (1)H NMR chemical shifts and NOEs in NOESY experiments after conversion into the corresponding esters with the chiral reagent 2-(2'-methoxy-1'-naphthyl)-3,4-dichlorobenzoic acid. All the metabolites showed antimicrobial activity against a fungus, Cladosporium herbarum, and Gram-positive bacteria, Bacillus subtilis and Staphylococcus aureus.