It happened on the 9100 block of Meredith in Highlands just before 4:30 a.m.
Deputies said the man ran to his neighbor's house and told them he shot his son in the leg and to call 911.
The father was placed in handcuffs and the son was transported to a hospital.
Investigators told ABC13 that deputies were called to the home Tuesday afternoon.
It's not clear what caused the shooting.