The bomb was planted along a highway route in front of a mosque in Narathiwat Province, 1,140 kilometres south of Bangkok.
Insurgents waited for the marines to go on their regular patrol before setting off the device, according to Police Lance Chakrit Chaiseesa.
Thailand's three Muslim-majority southern provinces have been embroiled in an insurgency since 2004 against the central government in the predominantly Buddhist nation.
More than 5,000 people been killed in the ongoing conflict.