Horst Seehofer, a longtime bitter rival of Angela Merkel, has confirmed he will step down as leader of the Bavarian Christian Social Union (CSU) in the latest high-profile resignation to shake German politics.

The move leaves both of Germany’s traditional conservative camps simultaneously searching for new leadership. It comes a fortnight after Merkel heralded a new era in German politics when she said she would not seek re-election as the head of the Christian Democratic Union (CDU).

Confirming days of speculation in the German media, Seehofer told a press conference on Monday: “I will resign from the post of party chairman of the CSU – this decision is definite.” The right-leaning Bavarian politician said he was stepping aside to “enable the renewal of my party”.

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Seehofer and Merkel had come under pressure following dismal results for the sister parties in regional elections last month. In Bavaria, the CSU had its worst showing in 60 years, followed by an almost equally disastrous result for Merkel’s CDU in Hesse.

Seehofer, who has led the CSU since 2008, said the precise timing of his departure was still being discussed. Earlier reports citing sources present at a Sunday meeting of the party leadership suggested a new leader would be chosen in January. Seehofer reportedly also told colleagues he would stand down as interior minister next year.

But Seehofer denied this interpretation on Monday, saying he intended to stay on in cabinet. “The post of interior minister is in no way affected by this decision. I am interior minister and will continue as such,” he said.

Seehofer has frequently clashed with Merkel over migration and has been a vocal opponent of her 2015 open-door policy, putting a severe strain on the seven decades-long partnership between the two parties. He nearly brought down the fractious coalition government this summer with demands for tighter immigration and border controls.

The stance, however, failed to win back voters from the far-right Alternative für Deutschland, and his constant bickering with Merkel was widely blamed for the CSU’s poor performance in Bavaria. Seehofer resisted calls for his resignation in the immediate aftermath of the poll, possibly waiting to see how Merkel would react.

Seehofer’s move mirrors Merkel’s decision to step down as party leader but stay on as chancellor, a post she has held since 2005, until elections scheduled in 2021. It is unclear whether either of Germany’s conservative heavyweights will be able to cling on until then.