The team's drivers - world champion Nico Rosberg and Lewis Hamilton - won 19 of the 21 races in 2016 and sealed the title with four races to spare.
Red Bull, though, gave Mercedes plenty to think about with their drivers Max Verstappen and Daniel Ricciardo often getting the very best out of the car.
But which team did most BBC Sport website readers choose as the best of the season? Here are the results...
They dominated the season and dominated the picks in the BBC Sport selector.
Statistically Mercedes swept aside all before them. As well as winning 90% of the races, a silver arrow also took pole position in all but one race - Monaco, where Ricciardo started at the front of the pack.
With Rosberg retired and Hamilton's new team-mate yet to be confirmed, their rivals can only hope that Mercedes may find it difficult to match such an all-conquering campaign as the new guy settles in, and new rules take effect.
After finishing fourth in the constructors' championship last season, Red Bull rose from that disappointment to cement themselves as the best of the rest.
They may not have had the package to truly challenge Mercedes but they certainly won plenty of fans, thanks to their drivers' skill on the track and character off it.
The fearless Verstappen completed 78 overtakes in 2016 - a new F1 record - while Ricciardo was consistently impressive in the second half of the season, finishing on the podium in seven of the last 11 races.
One to watch in 2017, especially as aerodynamics become a more important factor with the new rules. Do not forget who will be leading their design package - one Adrian Newey.
They may have a smaller budget than the leading teams in Formula 1, but Force India certainly knew how to get the most out of what they had as they finished a hugely impressive fourth in the constructors' championship.
Both Sergio Perez and Nico Hulkenberg consistently finished inside the top eight, with Perez also managing to climb the podium twice - finishing third in Monaco and Baku.
Jennie Gow: 1) Mercedes, 2) Red Bull, 3) Manor
Mercedes: "They have been on top of their game once again. There have been reliability issues for Hamilton but the team have an outstanding car and winning their third title gives them bragging rights this season. Let's see what they can do next year."
Manor: "The fact that they are even on the grid is impressive after all the challenges they have faced. The single point that they won in Austria is a major achievement and almost gave them 10th place in the championship. With such a small budget to work from and a small team compared to others, you have to take your hat off to the them and hope that despite losing 10th place to Sauber in Brazil, the team continue to flourish in 2017."
Tom Clarkson: 1) Mercedes, 2) Red Bull, 3) Force India
Red Bull: "Even with that botched pit-stop at Monaco, which cost Daniel Ricciardo the win, Red Bull Racing remains the racer's racing team. They're always aggressive strategically - just look at their switch to intermediates tyres in Brazil - and their rate of development is second to none."
Force India: "Given that the team operates on a quarter of the budget of F1's front-runners, what Force India achieved this year was extraordinary. The team maintained the performance gap to Mercedes and it maximised every opportunity. An example of how F1 teams could operate in a post-manufacturer era."
Nearly half of you felt Ferrari were the biggest underachievers of the season and it is hard to argue with that. For a team of their stature, a year without a single victory is hugely disappointing, even more so considering many had expected them to provide Mercedes with a genuine challenge for the title.
Sebastian Vettel's frustrations with the team's shortcomings was clear as the season wore on, with his strops over team radio broadcast to the world.
Ferrari will be hoping their fortunes, and Vettel's temper, improve considerably in 2017.
Jennie Gow: Haas
"Despite starting the season in style with points finishes in three of the first four races, that form hasn't continued and they have lost their way. Issue after issue has dogged the team and with a limited budget and manpower it will take quite a lot to turn the team around."
Tom Clarkson: Ferrari
"All of that money; all of those facilities; all of that driving talent… and yet Ferrari went backwards in 2016. Not only in terms of results, but in terms of work ethic - both at the factory and at the racetrack. With no obvious solution in sight, you have to feel for the good guys in the team."
It was another dominant season on the track for Mercedes as they won the constructors' championship for the third consecutive season.