The 5.0 magnitude earthquake struck at 2:55 a.m. local time (0055 GMT) in a remote part of Botswana north of the capital Gaborone, the US Geological Survey said.
The shallow tremor was only 6.2 miles (10 km) deep.
On Monday, Botswana was struck by its second biggest recorded earthquake when a magnitude 6.5 tremor shook an isolated area 250 km (155 miles) northwest Gaborone. That earthquake was felt in the capital, South Africa, Zimbabwe and Swaziland.
Strong earthquakes are rare in southern Africa.
No immediate information was available as to how the communities fared, but some minor casualties and structural damages were reported as far as 130 kilometers away from the earthquake's epicenter.
Villages and mines
Moiyabana village, 132 kilometers west of the quake's epicenter, was the only village reported to have felt the major brunt of the quake so far. Students at the village secondary school were affected by the quake which damaged some houses.
"As the earthquake happened during study time, a stampede broke out as everyone tried to escape and minor injuries were experienced," Tebogo Modiakgotla, spokesman for the local authority said.
The spokesman could not say if there had been any damage to the mines, or their surrounding communities, near the towns of Jwaneng, such as the Gaghoo Diamond mine.
The last time the country experienced any such quake was in 1952 when a 6.7 magnitude earthquake hit Maun in the northern part of the country.
AFP, Reuters
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