Mr Seehofer wants to put behind him the 2008 election, when the CSU scored its worst result in six decades with 43%.
That forced it into an alliance with the Free Democrats (FDP), who are also Ms Merkel’s coalition partners the national government.
The combined CDU/CSU bloc has about 40% support nationwide.
If they do win on 22 September they will need a partner to form a government,.
In Bavaria and in the Bundestag lower house of parliament, the FDP risks falling short of the 5% threshold for a seat in parliament, although their opinion poll results have improved in recent months.
A weak FDP showing in Bavaria might even scare conservatives elsewhere into giving their second vote to the FDP.
This potentially will weaken the share of votes that go to Merkel’s CDU.
Bavaria is home to 12.5m of Germany’s 80.5m people, is the only state with a regional party – the CSU – in the federal parliament.
When other regional conservative parties joined to form the CDU, the CSU remained separate, reflecting Bavaria’s strong regional identity. CSU lawmakers make up nearly a quarter of Merkel’s conservative bloc.
If Bavaria, home to carmakers BMW and Audi, were a country, it would have the eurozone’s sixth largest population and economy.
This allows it to exert pressure on national policy on issues ranging from energy and the family to the eurozone.
Bavarians consider themselves dedicated Europeans who have benefited from the single currency.
Calls within the CSU for Greece to leave the eurozone or to pay its civil servants in drachmas have not prevented it from backing Ms Merkel on bailouts.