Qatar Airways will suspend all flights to the Seychelles from 1 September.
Chief executive Akbar Al Baker says the decision was "due to commercial reasons, which is regretted".
The Doha-based carrier is to operate its last daily service to Mahe Island on 31 August.
The move follows Qatar Airways rival Etihad's purchase of a 40% stake in Air Seychelles in January 2012.
Etihad has a five-year management contract with Air Seychelles, and over the past 12 months it has expanded the latter's operation with 19 codeshares and four flights per week to Abu Dhabi.