The web site for Britannia Direct will be renamed www.thomsonflights.co.uk.
The UK's biggest operator sees cost-saving advantages in using the well-known Thomson brand to promote seat-only bookings as travellers seek flexible holidays.
"Our intention is to grow our flight-only business and we feel it's important to use the power of the Thomson brand," said Chris Motters-head, TUI UK's managing director. "It makes much more sense from a marketing point of view to put money behind promoting a single company."
Although Mottershead stressed there were no plans to rebrand the company's Lunn Poly retail chain, the decision puts a question mark over its long-term existence.
Over the past year, competitors Thomas Cook and First Choice have overhauled their brand strategies to ensure brochures, shops and planes all carry the same name.