Polls suggest that Bavaria's center-right Christian Social Union party, which has run the region for 61 years, is heading for its worst performance since the 1950s on Sunday. It appears to be losing voters on both the right and left despite enviable prosperity and unemployment at a rock bottom 2.8 percent.
The CSU, which is socially conservative and has taken a hard line on migration, exists only in Bavaria and is an important but often awkward sister to Merkel's Christian Democratic Union. The two parties govern Germany in an infighting-prone coalition with the center-left Social Democrats.
Though the CSU is unlikely to lose power in Bavaria altogether, a result like the one pollsters are forecasting would be humiliating. Speculation is rife that party leader Horst Seehofer, Germany's interior minister, could be forced out.
"The CSU has lost its cohesive power in Bavaria - it was able to win over voters from the right to the center-left," said Manfred Guellner, the head of the Forsa polling agency. "Now, because of its confrontational course with its sister party, with the chancellor, it has driven away the liberal center."
On the other side, the far-right Alternative for Germany is appealing to voters looking for an uncompromising anti-migration and law-and-order stance. About 9.5 million people are eligible to vote in the election for the state legislature in Munich.
For decades, the CSU attracted voters from across the spectrum, standing for a combination of modernity and tradition encapsulated by the slogan "Laptops and Lederhosen." It has held an absolute majority in the state legislature for all but five of the last 56 years and prides itself on punching above its weight in national politics.
Lately, that tradition has been evident largely in battles over migration between Seehofer and Merkel. Seehofer joined Merkel's Cabinet in March after giving up his job as Bavaria's governor to younger rival Markus Soeder following a long-running CSU power struggle.
"I can only say that voters don't appreciate it, and we can see that in the polls, when we argue with each other and they don't even understand what about," Merkel said last weekend as she reviewed the year since Germany's last national election.
In that vote, all three governing parties lost significant support and Alternative for Germany entered the national parliament.
The CSU, with its eyes firmly on the Bavarian election, doubled down on tough talk about migration. That has divided Merkel and Seehofer since 2015, when Seehofer assailed her decision to leave Germany's borders open as refugees and others crossed the Balkans.
Seehofer triggered the most serious crisis yet in Merkel's fourth-term government, when the pair sparred in June over whether to turn back small numbers of asylum-seekers at the German-Austrian border. The argument briefly threatened to bring down the administration and end his party's alliance with Merkel's.
He played a starring role in a second crisis last month, doggedly backing the head of Germany's domestic intelligence agency amid demands that he be removed for appearing to downplay recent far-right violence against migrants. Merkel's governing coalition needed two attempts to reach a compromise.
Seehofer's tactics have started annoying even conservatives who support his positions.
Volker Bouffier, a conservative seeking re-election as governor of neighboring Hesse state in an Oct. 28 election, remarked recently that the 69-year-old CSU leader has performed "outstanding services, but he has a tendency to make lone, surprising decisions."
Soeder, the new governor, has switched from even tougher talk on migration than Seehofer to trying to project an inclusive image as Bavarian leader. Polls suggest the switch hasn't been convincing.
They put support for the CSU as low as 33 percent - down from 47.7 percent in 2013, in an election held at the height of Merkel's popularity when Seehofer regained the absolute majority it lost five years earlier. Alternative for Germany didn't field candidates then, but looks set to win 10 percent or more this time.
The Greens are running second, with support of up to 18 percent, and the Social Democrats - struggling badly in national polls - could lose nearly half of the 20.6 percent they won five years ago.
Such a result would leave the CSU seeking either an ideologically difficult coalition with the left-leaning Greens or an alliance with one or more of the pro-business Free Democrats, the center-right Free Voters and the Social Democrats. A four-way coalition without the CSU might be mathematically possible, but is unlikely.
Soeder has blamed "politics in Berlin" for poor ratings in Bavaria. Seehofer is already insisting that he'll stay in his job after the election.
And Merkel, her authority already weakened by the government infighting and the ouster of a close ally as her party's parliamentary leader, will be hoping that poor election results in Bavaria and Hesse don't create new problems before a party convention in December where her leadership is due for renewal.
The government must "better present" its actions, she said Saturday. "I want to make my contribution to that."
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