The CSU is set to lose its absolute majority in the state parliament.
The Greens surged into second place and the anti-immigration AfD entered the state parliament for the first time.
The CSU has ruled Bavaria almost single-handedly since 1957, but has lost support as opinion becomes polarised over issues like migration.An exit poll for broadcaster ARD said the CSU (Christian Social Union) won 35.5%, with the left-leaning pro-immigration Greens on 19%.The Alternative for Germany (AfD) came fourth with 11%, behind a collective of independent candidates known as the Free Voters.
Mrs Merkel’s national coalition partners the centre-left Social Democrats trailed in fifth with 10%, their vote halved.
The AfD’s success in Bavaria has not been as great as in eastern Germany, but it appears to have taken large numbers of votes from the CSU.
But by echoing some of the AfD’s hardline policies such as on migration, the CSU also seems to have lost support to the left.