The two airlines made a statement on Monday, where the joint decision over the inter-island service was revealed.
The current agreement lasts until 16 March this year, after which the service will continue to be operated by Blue Islands.
Passengers with flights booked with Aurigny between 17 and 26 March will be automatically re-booked to Blue Islands flights. Passengers booked onto flights after those dates will have the option to have a refund or to fly on a Blue Islands flight.
It was announced last week that Blue Islands had entered into a memorandum of understanding with FlyBe.
Affected customers can contact Aurigny on 01481 822886.