The quake struck at 6:31 am (1231 GMT) with its epicenter in the Pacific Ocean at a depth of 46.8 kilometers, about 23 kilometers (14 miles) southwest of Puerto San Jose, the US Geological Survey said.
The Guatemalan Seismological Institute measured the quake at a magnitude of 6.7.
The country's civil protection authority said four people were injured but no one was reported dead due to the quake.
Spokesman Julio Sanchez of the National Disaster Reduction Coordinator told reporters nine homes, nine schools and eight roads were damaged and a bridge destroyed.
Culture Minister Jose Luis Chea said cracks appeared in the National Palace, a historic landmark in the capital.
Residents of El Salvador also felt the quake, with many people coming out of their houses for fear of aftershocks, according to authorities in that country.
On June 14, a 6.9-magnitude tremor hit Guatemala and southern Mexico, leaving five people dead, causing power outages and knocking down homes.
Guatemala is in a risk zone for earthquakes, located at a meeting of three tectonic plates.
The San Marcos department was hit by earthquakes in 2012 and 2014 that left dozens dead.
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