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The Anatolia news agency said Merkel had touched down in the southern city of Gaziantep from where she was scheduled to travel to Kahramanmaras to visit German troops who have been stationed there since January.
The 300 German soldiers are operating Patriot missiles as part of a NATO mission to protect the Turkish border from any spillover of the conflict in neighbouring Syria.
A German official said Syria will be a main talking point when Merkel meets with Prime Minister Recep Tayyip Erdogan and President Abdullah Gul in Ankara on Monday.
Turkey's EU ambitions will also be central in her discussions with the leaders.
Although Germany has opposed Turkey's bid to join the 27-nation bloc, favouring instead a "privileged partnership" between the two sides, Merkel on Saturday said she is in favour of a new chapter being opened in the negotiations.
Turkey's efforts to join the EU have stalled in recent years, largely because of the long-running dispute with Cyprus and fierce opposition from other EU member states.
Of the 35 so-called policy chapters EU candidates must negotiate, Turkey has opened talks on only 13.
The German official said new chapters that could be unblocked are those concerning economic and monetary policies.
The chancellor will end her visit Monday by taking part in a German-Turkish economic forum.