Acquiring good adhesion of ITO thin films on polymer substrate is a major concern, especially for space related applications. Delamination of ITO coating on these polymers can seriously damage the spacecraft. This paper presents the development of highly transparent and conducting ITO thin films on as-received and surface treated fluorinated ethylene propylene (FEP) and Kapton (R) substrates by reactive direct current magnetron sputtering. Stability of the ITO coating on FEP and Kapton (R) substrates was studied in simulated space environments. Environmental tests such as: relative humidity, thermal cycling and thermo vacuum were performed. Thermo optical properties and sheet resistance of ITO coated FEP and Kapton (R) substrates were studied before and after environmental tests. Optimized ITO coating with thickness of similar to 15 nm on FEP and Kapton (R) substrates showed sheet resistance in the range of 2-4 k Omega/sq. with high average transmittance and high IR emittance. Adhesion of ITO coating on FEP substrate was improved by Ar plasma etching. X-ray photoelectron spectroscopy and field emission scanning electron microscopic studies of etched FEP substrate showed defluorination and high roughness of the etched surface which helped for better adhesion of ITO coating. We demonstrated that ITO coated plasma etched FEP substrate showed no change in the sheet resistance and thermo-optical properties. Moreover, ITO coated etched FEP substrate showed good environmental stability than ITO coated untreated FEP substrates.