This study was carried out to compare and analyze the effect of Korean effective microorganism(KEM) and seafood amino acid fertilizer(SAF) application on apple on functional substances of fruit. Vitamin C in fruit of control and KEM/SAF treated were 29.3 and, 39.8 mg, respectively. Also active oxygen scavenging ability of those treatments measured with DPPH method were 40.6 and 54.1%, respectively. Vitamin E contents of those treatments were 2.51 and 2.50 mg, respectively. Sitosterol, a phytosterol, contents of those treatments were 4.79 and 5.41 mg, respectively. Proportion of sugars, fructose, glucose, and sucrose in the fruit of control were 36.1, 15.3 and 17.8%, respectively. Those of the fruit of KEM/SAF treated were 45.9, 13.2 and 18.8%, respectively. Malic acid contents of control and KEM/SAF treated fruits were 53.7 and 43.8%, respectively.