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The South Korean military says the soldier crossed the mid-eastern portion of the Military Demarcation Line -- which is located inside the Demilitarized Zone that divides the two countries -- at 10 a.m. local time.
It's not clear how or why he defected, but the South Korean military said it will investigate.
The soldier's defection follows that of a senior diplomat who abandoned his post at the country's embassy in the United Kingdom in August.
The defection comes amid a particularly tense time in North-South relations.
North Korea has flexed its military might frequently throughout 2016, conducting exercises and military tests at a faster pace than usual.
The zenith was reached earlier this month after North Korea conducted its fifth nuclear test ever -- and second this year -- prompting widespread condemnation from most of the international community.