The team, currently powered by Ferrari, will be supplied with current-year power units under the terms of a deal that will boost Marussia's long-term prospects, according to team principal John Booth.
"I am delighted to announce our new power unit partnership with Mercedes-Benz for the 2016 season and beyond," Booth said. "Although there were many factors governing our selection of an engine partner to help power us towards our long-term ambitions, ultimately the strength of the Mercedes-Benz package speaks for itself.
"2015 has been a rebuilding year in every aspect of our operation. Although we have not been able to make the incremental strides in competitiveness that the team has enjoyed in previous seasons, we have put in place a strong foundation from which to progress.
"Together with the potential we are seeing with our 2016 car in the wind tunnel, the Mercedes-Benz power unit will assist our return to aggressive performance development with effect from next season.
"I am also pleased to announce that we will resume our prior technical partnership with Williams Advanced Engineering, from whom we will receive the supply of transmission and suspension components. Combined with Mercedes-Benz power units, we are very excited about the strength of our new powertrain package and what it means for the long-term future of our team."
Marussia have used Ferrari power units since 2014, and Booth paid tribute to a relationship with the Italian team that went 'above and beyond' any contractual obligations.
"I would like to take this opportunity to thank Scuderia Ferrari for their support for our team over the past two seasons," he added.
"In 2014, together we shared in the momentous occasion of the team's first points and in 2015 Ferrari supported us to a degree that was above and beyond the requirements of our partnership agreement. Quite simply, we could not have returned to the grid without them pushing extremely hard to support the MR03B, at the same time as focusing on their own 2015 package."
Mercedes currently supply power units to Williams, Force India and Lotus. With Renault poised to take a controlling stake in the latter squad, the Marussia deal ensures Mercedes will have at least three customer teams in 2016 - the "ideal level in terms of technical and logistical capacity," according to Andy Cowell, managing director of Mercedes AMG HPP.
Toto Wolff, head of Mercedes-Benz motorsport, added: "Mercedes-Benz has a clear Formula One philosophy based around our works Silver Arrows team and supplying benchmark power units to independent customer teams.
"We believe this approach provides Formula One with greater strength in depth and ensures a deeper level of competitiveness throughout the field. In anticipation of Renault's takeover of the Lotus F1 Team, we are pleased to announce Manor Marussia as a new customer of Mercedes-Benz.
"It is a tenacious team with a fantastic competitive spirit, and we are all excited to see what step forward they can make next year with their new car coupled with the Mercedes-Benz Hybrid power unit."