British tourists Hannah Witheridge, 23, and David Miller, 24, both died of severe head injuries.
Police said the killers' DNA samples matched that found on the female victim's body. The murders happened last month.
The two accused, Win and Saw, both 21, underwent a reenactment at the crime scene with police yesterday, watched by a large crowd of onlookers.
A third man from Myanmar, Maw, 23, whose DNA also matched samples found on a cigarette butt, had not been charged as of yesterday.
The three men have also been charged with illegal entry, after they were found to have entered Thailand and resided unlawfully.
Prime Minister Prayut Chan-o-cha praised the police for the breakthrough in the much-publicised case saying he would soon reward them.
Citing the "confessions" of the two suspects, police said they entered Thailand about two weeks before the double murders at dawn on September 15 and worked at a pub.
Tourist business operators yesterday burst firecrackers to celebrate the arrests of the two suspects, and said they believed both men were the real culprits.
The murders were a major blow to the tourist-friendly image of Thailand.
National police chief Somyot Poompanmoung said evidence against both Win and Saw from surveillance camera footage and DNA identification had proved that they were "100 per cent the killers - not scapegoats".
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