American Eagle Bombardier CRJ-900ER aircraft seen at Phoenix Sky Harbor International Airport.American Eagle Bombardier CRJ-900ER aircraft seen at Phoenix Sky Harbor International Airport.

An enormous blow to the regional airline that was struggling with increasing costs and the industry's pilot shortage was caused by American Airlines' decision to drop Mesa Air.

American's chief financial officer and the president of American's regional brand American Eagle said in a staff note that they have concerns about Mesa's ability to be a reliable partner.

American Airlines, United Airlines and Delta Air Lines contract regional airlines to fly many shorter routes and they account for half of departures.

According to a securities filing, Mesa had a net loss of over $65 million in the first nine months of the year. The earnings report was delayed last week. Mesa didn't reply to the request for comment.

The Dallas/Fort Worth International Airport and Phoenix Sky Harbor International Airport are where American has its hub.

Envoy and PSA are two of American's wholly owned regional subsidiaries, as well as an independent regional carrier SkyWest. Air Wisconsin will start flying for the American Eagle brand earlier than planned.

The last Mesa flight for American will be on April 3, according to Kerr.

The flying previously done by Mesa will be backfilled by these high-quality regional carriers as well as our mainline operation, Kerr wrote.

United didn't immediately comment.