In Kisii County, the duo have to choose between Chris Obure and Joash Maangi for gubernatorial seat, with Uhuru believed to be solidly behind Mr. Obure.
"The president prefers Obure because of his immense political experience while Ruto will be confortable with Maangi. This could even threaten the campaign team," says Prof. Nyachieo Bogonko.
Maangi, who had recently declared his gubernatorial ambition, had initially agreed to deputise Obure.
In Nyamira County, another crucial region for the two, Uhuru is believed to be secretly backing former Kitutu Masaba MP Walter Nyambati for Governor while Ruto is keen to have businessman Charles Mochama.
"It will not be business as usual. The two principals seems to be having their preferred candidates and this is detrimental in the campaign. Already we have cracks in the two counties," added a Jubilee coordinator from Kisii region who spoke on condition of anonimity.
In 2013, ODM leader Raila Odinga scored overwhelmingly from the region that Jubilee is keen to capture.