This study aimed to determine the photosynthesis and growth characteristics of Peucedanum japonicum T. grown under aquaponics in a plant factory (AP) by comparing those grown under hydroponic cultivation system (HP). The AP system raised 30 fishes at a density of 10.6 kg·m-3 in a 367.5 L tank, and at HP, nutrient solution was controlled with EC 1.3 dS·m-1 and pH 6.5. The pH level ranged from 4.0 to 7.1 for the AP system and 4.0 to 7.4 for the HP system. The pH level in the AP began to decrease with an increase in nitrate nitrogen (NO3-N) and lasted bellower than pH 5.5 for 15–67 DAT. It was found that ammonium nitrogen (NH4-N) continued to increase even under low pH conditions. EC was maintained at 1.3 to 1.5 dS·m-1 in both systems. The concentration of major mineral elements in the fish tank was higher than that of the hydroponics, except for K and Mg. There was no significant difference in the photosynthesis characteristics, but the PIABS parameters were 30.4% lower in the AP compared to the HP at the 34DAT and 12.0% lower at the 74DAT. There was no significant difference in the growth characteristics, but the petiole length was 56% longer in the leaf grown under the AP system. While there was no significant difference in the fresh and dry weights of leaf and root, the leaf area ratio was 36.43% higher in the AP system. All the integrated results suggest that aquaponics is a highly-sustainable farming to safely produce food by recycling agricultural by-products, and to produce Peucedanum japonicum as much as hydroponics under a proper fish density and pH level.