Max Biaggi and Carlos Checa raced for the team from 1999 to 2002. Max Biaggi achieved a total of 9 race wins in that period, first riding the Yamaha YZR500 and later the Yamaha YZR-M1 in 2002.
In 2003, Checa was joined by Marco Melandri. The team had an average season with no wins or podiums.
For 2004 Valentino Rossi joined Carlos Checa at the team. Rossi got 9 wins and won the championship.
Colin Edwards joined the team for 2005. Rossi once again won the championship, collecting 11 wins.
Both riders stayed with the team for 2006. Rossi earned 5 wins and finished 2nd in the championship.
For the 2007 season, both riders remained with the team riding the new 800cc Yamaha YZR-M1. Rossi had 4 wins and finished the season 3rd overall.
For 2008, Yamaha had a unique line-up with Valentino Rossi and Jorge Lorenzo. Although the pair were fighting for the title from different pit boxes (as Valentino Rossi chose to use Bridgestone tyres and as Jorge Lorenzo continued with Michelin), Yamaha operated as one brand and not two separate manufacturers. The title was won dominantly by the returning hero Rossi who won 9 of the 18 races and finished on the podium in every race except for two. Even though this was the learning year for Jorge Lorenzo, the Spanish star was able to cruise to victory at Estoril and finished 4th in the championship. In 2009, Yamaha dominated MotoGP with Rossi winning the title and Lorenzo finishing second. The pair won 10 out of the 17 races, and Yamaha won the Constructors' Championship.