The unnamed pair were the only professionals out of 18 to be unvaccinated.
This year’s show will host a live audience with hundreds of fans gathering in the studio each week.
The unvaccinated dancers have sparked fears of an outbreak that could potentially halt the show’s production.
Bosses are already dealing with a Covid crisis after one pro tested positive earlier this week. They are currently in isolation and their celebrity pairing is likely to get a new partner.
As part of Covid protocol pro dancers stay at a hotel and are tested multiple times a week.
A source said: “Strictly already has to jump through hoops just to be able to broadcast.
“The dancers who won’t get vaccinated have been a topic of conversation among cast and crew for weeks — even before the positive test.
“There were vocal protests from celebrities that they didn’t want to be paired with them.
“It’s a headache for bosses but employers cannot force workers to get jabbed.
“Their stance has also miffed other pros, some of whom did not want to get jabbed but did so for the good of the show.
“Throw in one dancer already in isolation, and anxiety is at an all-time high.”
The new series of Strictly Come Dancing will start at 7.45pm tonight on BBC One.
The show stars Dan Walker, Ugo Monye, Sara Davies, Nina Wadia, John Waite, Robert Webb, Rose Ayling- Ellis, Adam Peaty, Judi Love, Tom Fletcher, Tilly Ramsay,, Rhys Stephenson, AJ Odudu, Katie McGlynn and Greg Wise.
A BBC spokesman said last night: “We do not comment on speculation of somebody’s Covid vaccination status. Production has, and will, continue to follow strict government guidelines to ensure the safety of all on the show.”