A government source told ABC News that an off-duty JetBlue pilot who was traveling on the flight helped land the plane in Texas.
"At roughly 10 a.m. CT/11 a.m. ET, the pilot in command elected to divert to Amarillo, Texas, for a medical situation involving the captain," JetBlue said in a statement.
"Another captain, traveling off duty, entered the flight deck prior to landing at Amarillo, and took over the duties of the ill crewmember once on the ground," the statement said. "The aircraft arrived Amarillo at 10:11 am CT, and the crewmember was removed from the aircraft and taken to a local medical facility."
The captain is now in FBI custody.
Today's commotion was the latest sky-high incident to interrupt a flight. On March 9, an American Airlines flight headed from Dallas-Fort Worth to Chicago returned to the gate just prior to take off when a female flight attendant began making inflammatory remarks over the public address system. Passengers intervened and restrained the flight attendant before Dallas airport police boarded the flight.