The propeller plane was on a training flight when it crashed into the Mediterranean near the coastal town of San Javier in the region of Murcia, it said in a tweet. The plane belonged to military training academy.
The pair were named as flight instructor Daniel Melero and trainee pilot Rosa María Almirón.
Nuestro pésame a los familiares, amigos y compañeros del comandante Daniel Melero y la alférez alumna Rosa María Almirón, de la Academia General del @EjercitoAire,
fallecidos hoy en un accidente aéreo sobre el Mar Menor en San Javier (Murcia).
— Ministerio Interior (@interiorgob) September 18, 2019
San Javier city hall ordered area beaches to be closed until further notice in the wake of the accident.
Last month a military flight instructor died after his small jet crashed at sea in the same area.
He was able to eject before the plane hit the water but his remains were later found.