Exit polls showed the ruling Christian Social Union, the Bavarian affiliated party of Merkel's Christian Democrats, received an absolute majority of seats in the regional parliament, capturing 49-percent of the vote, Local.de reported.
The CSU has governed Bavaria for 56 years.
The CSU is led by state Premier Horst Seehofer. The report said Merkel campaigned heavily in Bavaria's famous beer tents, telling voters a big win would give momentum to her bid for a third term.
Seehofer was challenged by Munich Mayor Christian Ude of the center-left Social Democratic Party, Euronews.com reported.
Ude was polling at 18 to 20 percent as voters went to the polls.
On Sept. 22, Germany will vote to elect a new Parliament.