Their deaths came during a night of violence across a region plagued by unrest for over a decade as ethnic Malay rebels battle Thai troops for more autonomy from the Buddhist-majority state.
Colonel Yutanam Petchmoang, deputy spokesman of the southern army, said the two militants died while transporting an improvised explosive device in Sabayoi district, Songkhla province.
"They were on a motorbike," he said. "We have in their records that they were local militant sympathisers."
The military said insurgents launched a string of gun and grenade attacks across Thailand's so-called Deep South on Wednesday night with 13 separate incidents recorded.
Bombs and drive-by shootings are a weekly occurence in Thailand's south where the fighting has claimed more than 6,800 lives -- mostly civilians -- since 2004.
Both sides have been accused of rights abuses and atrocities.
The country's ethnic Malay southernmost border provinces, former Muslim sultanates, were annexed by Bangkok more than a century ago.
The junta, which seized power in 2014, has held several rounds of negotiations with one group that claims to represent the insurgents, the Mara Patani.
But the talks have failed to make headway and many doubt the rebel negotiators have clout over fighters on the ground.
The biggest faction that controls the most fighters -- the Barisan Revolusi Nasional (BRN) -- issued a rare statement earlier this month restating its opposition to the current Thai army-led peace talks.
The military refuse to talk to the BRN even though most analysts say Mara Patani has little sway over the militants doing the actual fighting.
The BRN has said it will only come to the table if a third-party mediates the talks and international observers are allowed -- demands Thailand's military have repeatedly refused to accept.
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