The department is now trying to ensure that the couple is freed quickly.
"Dirco can now confirm the kidnapped pair in Yemen are South Africans. Officials are intervening... to engage all role players," said Dirco spokesperson Clayson Monyela.
The pair was kidnapped in Yemen's central province of Taiz on Monday by unknown gunmen in front of a hotel in the town of Howban, about 250km south of the capital Sana'a.
Foreigners are frequently kidnapped in Yemen by al-Qaeda militants or tribesmen, who ask for ransoms for the release of their prisoners. Most of the kidnapped have been freed unharmed.
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