Hi Pedmar,

The ships for the first trip to America were ships from the Castilian Navy.
They carried the Castilian flag and the "Bandera Capitana del Almirante de Castilla" (the flag of the Castilian Admiral) wich was a white flag with a green cross in the midle and with the letter F at the left side and the letter Y at the right side of it.

official web page of the Spanish Navy