During the war, the FW-200 Condor flew in standard Luftwaffe military camouflage. The undersurfaces were painted in RLM 65 (1941) Hellblau, while the upper and side surfaces received sharply broken camouflage spots in the colors RLM 70 Schwarzgrün and RLM 71 Dunkelgrün. Transport aircraft transferred from Lufthansa were also painted. The aircraft operating in the KG 40 received a marine paint, which featured different shades of green on the top and side surfaces of the airframe. In this version, the colors RLM 72 Grün and RLM 73 Grün were used. Some aircraft used for night mine-laying operations off the coast of Great Britain were painted underneath in RLM 22 Schwarz black. At least one aircraft operating in the winter of 1943 near Stalingrad was painted white on the top and side surfaces.
Several dozen machines that flew over the Arctic Ocean in 1944 received additional camouflage on the upper and side surfaces of the glider, the so-called Wellenmuster, consisting of irregular zigzags applied with RLM 76 Lichtblau paint on a green background. Nationality insignia - black beam crosses with white outline - were drawn on both sides of the wings and fuselage. A black swastika with a white outline was placed on the vertical stabilizer. Several aircraft operating on the Eastern Front received yellow quick identification marks typical of the Luftwaffe aircraft in Russia. It was a narrow yellow stripe on the fuselage and yellow wingtips on the bottom painted with RLM 04 Gelb. On the sides of the fuselage, and also, in many cases, on the lower part of the wings, a letter code was drawn. Some of the aircraft had factory codes, the so-called Stammkennzeichen, consisting of four letters drawn in black in accordance with the following pattern: KF + QB. Under the wings, the letters of the code were placed as follows: K + F and Q + B. After the vehicle was delivered to the combat unit, these letters were replaced with a four-digit unit code (three letters and one number), but very often they left Stammkennzeichen, neglecting the application of the code.
The first two characters of the unit code designated a regiment or a separate squadron, F8 - KG 40, or A6 - Aufkl.Gr.120. The third letter was drawn directly behind the fuselage cross and represented the individual designation of the aircraft as part of the squadron, it was painted with the color assigned to this squadron, or in black with a squadron color outline, and the black letter denoted the squadron or division headquarters (letters from A to F). These designations were most often repeated under the wings. In front of the fuselage, the emblems of the unit were drawn. Here, behind the cockpit, the KG 40 emblem was usually placed - a globe (black and white or black and blue), circled in a yellow ring (a reminder of the Condor records set before the war). The early version of the emblem included the outlines of Eurasia and Africa, after the entry into the war of the United States of America, the outlines of two Americas appeared on the globe. Aircraft belonging to Blindflugschule 36 carried emblems painted under the front cockpit visor.
On the front of the nose of the fuselage, the aircraft's own name was sometimes applied, usually in white. These were mainly the names of planets (Venus, Jupiter, Mars) or stars (Sirius, Polaris). Symbols were placed on the vertical stabilizer, denoting the victories of the aircraft crew. White beams - for each completed combat mission, and the silhouettes of the ships along with the date - as a designation of sunken enemy ships. Inside the fuselage and landing gear niches, FW-200s were painted in the standard Luftwaffe color RLM 02 Grau. The propeller blades were painted with RLM 70 Schwarzgrün paint, the same paint was most often used for painting the propeller cocks. The wheel rims were painted in RLM 66 Schwarzgrau.