The shooting victims, aged 27 and 17, were found with their hands tied behind their backs and gunshot wounds to their heads in Narathiwat -- one of three provinces in the Thai south where thousands have died in eight years of unrest.
Police said investigations into the deaths would consider a potential drug-related conflict as well as the insurgency.
Also on Sunday morning in the same province, a nine-year-old Muslim boy accidentally stepped on a bomb planted at the side of the road as he walked home from a grocery shop with two friends.
The explosion tore off the child's left leg and left the other boys, both also aged nine, with minor injuries.
A complex insurgency, without clearly stated aims, has plagued Thailand's far south near the border with Malaysia since 2004, claiming thousands of lives, both Buddhist and Muslim, with near-daily bomb or gun attacks.