The daily flight between City of Derry Airport and Dublin was withdrawn yesterday.
Aer Arann said it had ended the service because it was no longer commercially viable without Irish government subsidies.
The airline company has also ceased operating regional flights to Galway, Sligo and Knock.
The previous Minister for Transport Noel Dempsey announced in January that the contracts would end in July.
The airline has confirmed it continues to run all of its other routes.
Public Service Obligation (PSO) contracts at Kerry and Donegal were not affected by the Department of Transport’s decision in April.