Attackers killed a 52-year-old school caretaker and critically injured his 41-year-old wife at a rubber plantation in Narathiwat, one of three restive provinces near the border with Malaysia.
In a separate attack in the same province, a 40-year-old Muslim man was shot dead at a tea shop.
A complex insurgency, waged without clearly stated aims, has riven Thailand's far south for years, claiming thousands of lives, both Buddhist and Muslim, and resulting in a heavy military presence in the region.
Last month an incident in which four Muslim civilians, including an elderly man and an 18-year-old boy, were shot dead by state paramilitaries sparked an official investigation and local outrage at army activity in the area.
Army chief General Prayut Chan-O-Cha urged the military to be more cautious in the south following that shooting, but said the 40,000 soldiers and 20,000 other security officials in the south were "not sent to fight".
"You must understand that solving the southern unrest will not be through fighting but through understanding," he added.
Around 5,000 people have been killed and 8,300 wounded since the unrest began in 2004, according to local conflict monitor Deep South Watch.
People in the region complain of a long history of discrimination against ethnic Malay Muslims by authorities in the Buddhist-majority nation, including alleged abuses by the armed forces.