Authorities said neither quake left major damage nor victims.
The U.S. Geological Survey reported a 6.9 magnitude quake hit the waters between the Baja peninsula and the northern state of Sonora at 12:15 a.m. local time.
Residents in the city of Hermosillo woke up as their beds swayed and their ceiling fans shook. Luis Enrique Cordova, director of emergency services in Sonora, said confused residents clogged the phone lines of the civil protection office in Hermosillo, the largest city and capital of the state, where some 700,000 people live. But Cordova said no major damages have been detected in the region.
"I was on my bed, leaning against the wall, and the fans kept moving non-stop, side to side," said Carlos Morales, a teacher in Hermosillo.
The temblor was centered 82 miles (133 kilometers) northeast of Guerrero Negro, and 133 miles (215 kilometers) west of Hermosillo, and it hit some 6.4 miles (10.3 kilometers) below the surface.
It follows a 6.4 magnitude quake which struck a sparsely populated area in the mountains of western Mexico on Wednesday, and caused multi-story buildings to sway more than 200 miles (322 kilometers) away in Mexico City.
Wednesday's temblor was the latest in a series of strong shakes to hit Mexico City since a powerful 7.4-magnitude quake hit southern Mexico three weeks ago. But this was not an aftershock of that one, USGS geophysicist Dale Grant said.
Last month's big earthquake was felt strongly in the nation's capital, and it damaged hundreds of homes and killed at least two people near the border between Guerrero and Oaxaca states. Mexico's seismological service said that quake has been followed by close to 400 aftershocks, including one of magnitude 6.0.