The auction is the latest move by Hostess to offload its various business units after a bankruptcy judge approved a liquidation of the company after it failed to reach an agreement with its unions in 2012.
(Read More: The Fight to Buy Hostess: Main Street vs. Wall Street.)
On Wednesday, Flowers was named the winning bidder for the rest of Hostess' five bread brands — including Wonder Bread, Nature's Pride, and Merita — as well as 20 bakeries and various other assets. The bid stood at $355 million — plus an additional $5 million for certain licensing agreements — and remained unchallenged ahead of a proposed auction, sources said. Flowers Foods stock rose as much as 4 percent on the news in intraday trading Wednesday.
(Read More:At Hostess, Everything's for Sale but the Kitchen Sink.)
In March, marquee Hostess brands like Twinkies and Ding Dongs will be auctioned in a similar, court-sanctioned process. If all the sales close this spring, production of the brands could begin again around June, a person familiar with the matter has said.
—By CNBC's Kayla Tausche; Follow her on Twitter: @KaylaTausche