In addition to the order made by the Luftwaffe, the German Navy's Marineflieger also received 112 of the IDS variant in the anti-shipping and marine reconnaissance roles, again replacing the Starfighter. These equipped two wings, each with a nominal strength of 48 aircraft. The principal anti-ship weapon was the AS.34 Kormoran anti-ship missle, which were initially supplemented by unguided bombs and BL755 cluster bombs, and later by AGM-88 HARM anti-radar missiles. Pods fitted with panoramic optical cameras and an infra-red line scan were carried for the reconnaissance mission.

The end of the Cold War and the signing of the CFE Treaty gave rise to a requirement for Germany to reduce the size of its armed forces, including the number of combat aircraft. To meet this need, one of the Marineflieger's Tornado wings was disbanded on 1 January 1994; its aircraft replaced the Phantoms of a Luftwaffe reconnaissance wing. The second wing was enlarged and continued in the anti-shipping, reconnaissance and anti-radar roles until it was disbanded in 2005 with its aircraft and duties passed on to the Luftwaffe.

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