In manufacturing of flatfish skin collagen peptide (FSCP) and flatfish protein hydrolysate (FPH) by reuse of dead flatfish from fish farm in Jeju island, the industrial process was optimized with the laboratory scale research and the on-field process. Segmented unit processes from raw material incoming to shipment were established to produce commercial product of FSCP and FPH. Total plate counts of FSCP were twenty five times of FPH, but food poisoning bacteria were not detected in two samples. FSCP and FPH were safe from heavy metal such as Pb(II), Cd(II) and Hg(II). The residual contents of antibiotics and disinfection matter in FSCP and FPH were not detected. The optimized process for mass production made the one-third of the running time and two times of the yield. From economic analysis, the production cost was estimated to 22,000 and 12,000 won/kg for FSCP and FPH, respectively. Therefore the product from the reuse of dead flatfish was expected to have a considerable competitive price and high added-value functional food material compared with other commercially available fish products.