The vote is being seen as a referendum on the Chancellor and her government with the Christian Social Union (CSU) - coalition partner and Bavarian sister party of her Christian Democratic Union (CDU) - going under the spotlight.
The result could have a massive impact on the fractious coalition if the CSU loses its absolute majority amid Germany’s rise in populism and anti-government sentiment.
The parties were staunch allies until a public row over migration policy marred the partnership and nearly brought down the fragile coalition earlier this year.
CSU leaders have been openly critical of Mrs Merkel's migrant policy and fear handing yet more of the party’s political ground to the right-wing, anti-immigrant Alternative for Germany (AfD), which exceeded expectations in national elections a year ago.
Mrs Merkel’s government will be damaged, possibly fatally, if the CSU performs badly at the ballot box and heavy losses are blamed on CSU leader Horst Seehofer, interior minister in her cabinet.
Teneo Intelligence's Macro Research predicts the CSU will lose its traditional absolute majority and have a knock-on effect on the party leadership.
It said: “The CSU will either require a coalition partner, or, depending on the magnitude of its losses, might even have to go into opposition.
"Rather than Bavarian Minister President Markus Soeder, the CSU will blame its leader, Merkel's Federal Interior Minister Horst Seehofer.
"Bavarian attempts to oust him have the potential to cause another protracted government crisis in Berlin."
Bavaria is a key strategic voting ground as it is the largest state, and one of the richest, in Germany.
It is the home to around 16 percent of the German population and accounts for 18.3 percent of the country's gross domestic product.
One analyst said: “Bavaria matters. It could become an important milestone, either imminently or in the future."
ING economist Carsten Brzeski said: “Since the start of the new government in March this year, German politics have been hijacked by the forthcoming regional elections in Bavaria.
"In a bid to defend its absolute majority in Bavaria, the CSU has been openly criticising Merkel, starting several inner-coalition conflicts which almost led to a collapse of the government.
"While the CSU tried to make the election a kind of referendum on Merkel's stance on refugees, the continuous nagging and trouble-seeking in Berlin, initiated by the CSU, has completely turned this around.
“According to the trend of latest opinion polls, the CSU's strategy to distance itself from Merkel in order to prevent a rise of the AfD in Bavaria seems to have been a double failure.”
A poll published by German broadcaster ARD last week showed support for the CSU had fallen to 33 percent, down from a typical vote share of around 50 percent.
The poll showed the Greens Party in second place, with 18 percent voter support, ahead of the Social Democrats - a coalition partner of the CDU and CSU in Berlin - with 11 percent and the far-right AfD with 10 percent.
If the polls are accurate, the CSU could see its worst performance since 1950, when it received 27.4 percent of the vote.
Greg Fuzesi, an economist at JPMorgan said: "The election will also set the tone for further CDU-CSU cooperation at the federal level and could put further pressure on Merkel herself.
"A test could come at the CDU party conference in December, when Merkel is likely to stand for re-election as leader of the CDU.
“At this stage, it is unlikely any high-profile candidate would run against her, but this will be another test of her authority."