Flylolo, which is based in Sussex in the UK, has blamed the cancellation of 140 flights and 2,000 bookings on uncertainties caused by Brexit.
The firm launched non-stop flights to Skiathos in Greece last year but has now ditched all of its services from Southampton.
A statement from the company says: “It is with the greatest regret that I have to advise that we are cancelling our entire Southampton programme for this summer.
“We had agreed many months ago a flying programme for an Airbus 319 flight operator, but the aircraft owner did not want to finalise our agreement whilst the Brexit situation was still undecided.
“We anticipated that the Brexit agreement would pass last November, we are still waiting for a final outcome which is still pending.
“The aircraft operator has decided he cannot risk putting the aircraft into the UK until there is certainty. He has advised us he is not prepared to go forward on the arrangements.”
It is not known how many Channel Islanders are affected by this withdrawal.
