Alaska Airlines plans to close its New York pilot base in September to reinforce its West Coast fleet, asking more than 100 pilots to relocate to California in a matter of months.



Alaska struck a $2.6 billion deal to acquire Virgin America in April 2016 and grew Alaska into the fifth largest airline in the U.S., serving over 44 million passengers in 2017.



Pilots that fly routes from New York area airports, John F. Kennedy International Airport, Newark Liberty International Airport and LaGuardia Airport, will relocate and deploy from West Coast hubs this fall. The company's aircraft will still serve New York.

Prior to the merger, Virgin America competed with established airlines on this transcontinental route for over a decade, by advertising as the cool, alternative airline of Silicon Valley.



"This was a difficult decision — but a necessary one — based on the need to match our pilot staffing with the geographic areas on the West Coast where we deploy our aircraft every day. All of our JFK-based pilots are being offered the opportunity to transfer to either Los Angeles or San Francisco," a spokesperson for the airline told CNBC via email. Alaska offers 14 flights a day to JFK and the company says it will add another in July.

Mid-continental and East Coast routes accounted for 4 percent of the Alaska's flight composition back in 2013, but it climbed to 10 percent after the merger. In that same timeframe, Alaska's California presence has climbed from 15 percent to 25 percent in network composition, which could increase after the transition.



Alaska now serves 115-plus destinations from seven hubs along the West Coast. The airline leads domestic seat share in Seattle, Portland and Anchorage. It ranks second in San Francisco and fifth at Los Angeles International Airport.

United Airlines still accounts for more than 40,000 seats per day at SFO, nearly four times more than Alaska. At Seattle-Tacoma International Airport, Delta has increased its stake by offering 50-plus destinations including eight foreign countries. Alaska will also face tough competition down the road in Hawaii, as Southwest Airlines is launching a low-cost service from four California cities, including inter-island routes.