A powerful 6.7 magnitude quake struck Ecuador's northeastern coast just before noon, the country's Geophysical Institute said.
That followed a 6.7 magnitude earthquake that struck in approximately the same region at 2:57 am local time (0757 GMT).
Six people were injured in the morning quake, only one seriously, officials said. Physical damage was minor.
There were no initial reports of victims or damages in the second quake.
The epicenter of the midday quake, which struck at 11:47 am (1647 GMT), was located in the northwestern coastal province of Esmeraldas near the border with Colombia, the Institute said.
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The US Geological Survey, which monitors earthquakes worldwide, reported that the second quake measured 6.8 on the moment magnitude scale.
The quake's epicenter was located 24 kilometers (14 miles) north-west of the town of Rosa Zarate, and 46 kilometers (28 miles) east-southeast of the town of Muisne, the USGS said.
Today's quakes are aftershocks of a powerful 7.8 quake on April 16 that flattened buildings and buckled roads in the area around Esmeraldas. Some 29,000 people were displaced by that quake.
President Rafael Correa took to Twitter to calm his jittery people.
He earlier told Ecuadorans that "nature is testing us," and warned that "there will be more aftershocks" of magnitude 6 or more.
Both earthquakes were felt as far away as the Colombian city of Cali, some 480 kilometers (300 miles) to the northeast, and the capital Quito, where homes and government buildings emptied out.
Fearful of more aftershocks, many Quito residents lingered in area parks.