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The companies currently have a so-called interline agreement that allows customers to buy connecting flights on each other's planes on one ticket.
Such agreements help increase revenue as airlines can offer more destinations without having to service all the planes themselves.
The airlines will not accept new interline sales with each other from Monday, the companies said on Monday.
The carriers also said customers using their reciprocal frequent-flyer programs would no longer earn miles or points when traveling on eligible routes, effective April 1.
The carriers did not say why they were ending the agreements. Both could not be immediately reached for comment outside regular U.S. business hours.
The frequent-flyer program agreement between the two includes select routes from Boston Logan International Airport and New York's John F. Kennedy International Airport.
All American Airlines' "AAdvantage" miles or JetBlue's "TrueBlue" points already accrued through this partnership will be credited to customers' accounts and will not be affected, the carriers said.
Reporting by Sagarika Jaisinghani in Bangalore; Editing by Savio D'Souza and Saumyadeb Chakrabarty