In this study, the morphology and antioxidant content of shiitake mushrooms (Lentinula edodes) cultivated in smart farms and general farms have been compared. With regard to morphology, mushrooms produced in the smart farm system exhibited a slightly thicker and wider pileus and thicker and longer stipe than those in the general farm system. The stipe in the mushrooms from moderate-sized farms was harder, because the low relative humidity of cultivation rooms could induce mushroom tissue to harden. With regard to the antioxidant content, the free radical scavenging activity was evaluated by the DPPH assay. Among the various treatments, hot water extracts of freeze-dried shiitake produced from smart farms exhibited the highest DPPH value of 37.8%. In contrast, the lowest activity of 12.2% was observed in a 70% fermented alcohol extract of shiitake that was dried by hot air. The polyphenol content was higher in hot water extracts than in 70% fermented alcohol extracts. Additionally, the polyphenol content was higher in the freeze-dried samples than in hot-air dried ones. The smart-farm system was preferred over the general cropping system for cultivating shiitake mushrooms, because the antioxidant activity and polyphenol content of mushrooms from the smart-farm system was better; the functionality of this system was more improved than that of the general cropping system, and it enables mushrooms to be cultivated more efficiently. The antioxidant content is represented as the mean±SD of three replicates. Different letters indicate significant differences among samples, i.e., p<0.05.