Whole mycelia of marine fungal strain Penicillium citrinum CBMAI 1186, both free and immobilized on cotton (Gossypium sp.), fibroin (Bombyx mori) and a local kapok (Ceiba speciosa), catalyzed the chemoselective reduction of chalcones [(E)-3-(4-fluorophenyl)-1-phenylprop-2-en-1-one 3a, (E)-3-(4-bromophenyl)-1-phenylprop-2-en-1-one 3b, (E)-3-(4-methoxyphenyl)-1-phenylprop-2-en-1-one 3c, (E)-3-(4-methoxyphenyl)-1-phenylprop-2-en-1-one 3d, (E)-3-(3-nitrophenyl)-1-phenylprop-2-en-1-one 3e] to dihydrochalcones [3-(4-fluorophenyl)-1-phenylpropan-1-one 4a, 3-(4-bromophenyl)-1-phenylpropan-1-one 4b, 3-(4-methoxyphenyl)-1-phenylpropan-1-one 4c, 1-(4-methoxyphenyl)-3-phenylpropan-1-one 4d, 3-(3-nitrophenyl)-1-phenylpropan-1-one 4e] in good yields. The immobilized fungus and free whole mycelium showed a similar behavior in the conversion of the chalcones. The hyphae immobilized on biopolymers were active in biotransforming the chalcones after being preserved for 30 days in refrigerator. Scanning electron micrographs showed that the cells of marine fungus P. citrinum CBMAI 1186 were intertwined with the fibers of the supports, allowing fast separation from the reaction media and easing reuse of the biocatalyst. It is concluded that marine fungus P. citrinum CBMAI 1186 presents potential for the biotransformations of reduction of chalcones (3a–e). This paper describes the first reported use of immobilized marine fungus in reactions catalyzed by enoate reductases.