Detectives claim an off-duty officer had spotted the pair shining beams at aircraft descending into Malaga airport.
The 41-year-old man and his 15-year-old boy were on their hotel room’s balcony in Torremolinos at the time.
Several pilots are believed to have complained about being dazzled with a green laser pointer as they prepared to land.
The emergency services managed to locate and identify the holidaymakers, and two laser pens were seized.
A statement from Spain’s National Police said the “very serious violation” could result in a fine of at least £27,000 and up to £540,000.
In February, the UK Government said people shining laser pens at pilots or drivers would face hefty fines or even prison under tough new powers.
Transport Secretary Chris Grayling warned the practice was “incredibly dangerous” as it risked causing temporary blindness.
Offenders in the UK face fines of up to £2,500, but investigators must prove a person has endangered an aircraft.