This study aims to estimate the Green-House-Gas emissions from domestic farmed flounder in the southern sea and Jeju-Do, where is mainly produced, by the assessment of energy consumptions and GHG emissions from domestic fish farms for establishing reduce standards of greenhouse gas from a sustainable perspective. It needs to analyze such GHG emission components as feed, electricity, fuel, fixed capital, fish respiration, and liquid oxygen in two locations by 4 stage running water type farm size of small, small and medium, large and medium, large scale. The result showed that the mean GHG emissions were 36.83 kg·CO2/year in the southern sea and 24.33 kg·CO2/year in Jeju-Do, respectively, in the stage of production per fish 1kg at 2 locations and farm size from domestic farmed flounders, and it will give to be useful for policy, planning, and regulation of aquaculture development with establishing GHG reduction standards.