Glasgow-based Loganair serves routes from the mainland to the Scottish islands and will run them under its own name – and with a tartan tailfin - from September 1 2017.
The airline is most famous for its “times subject to tide” flights landing on the beach airport at Barra and the world’s shortest scheduled flight, linking the Orkney islands of Westray and Papa Westray, with daily services taking only two minutes.
The axing of the partnership with Flybe will see Loganair establish its own reservations system from March.
Loganair told the BBC it had been happy with the arrangement but that there were elements it wished to offer customers, like free checked in bags and child discounts, that “don’t fit comfortably with the Flybe brand”.
Loganair earlier had a franchise agreement with British Airways from 1993 until it struck the Flybe deal in 2007. The carrier said it would continue to serve Scotland and would reveal plans “in due course”, but confirmed that it would provide more than 1,000 flights a week on 46 routes, including services to London, Norwich, Manchester, Dublin, and Bergen.