At the moment, there are 2 active ferry routes between Germany and Denmark: Rostock - Gedser and Puttgarden - Rødby. Both routes are served by the Scandlines ferry company.
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The best way to get from Denmark to Germany is to fly which takes 2h 42m and costs 450 kr - 2500 kr. Alternatively, you can train via Hamburg, which costs 600 kr - 1200 kr and takes 7h 8m, you could also bus, which costs 340 kr - 480 kr and takes 9h 8m.