Upon arriving in San Jose, Thornton improved the Sharks' fortunes and found instant chemistry with winger Jonathan Cheechoo. During the absence of usual alternate captain Alyn McCauley from the San Jose line-up, Thornton donned the "A" for the first time as a Shark in a game against the Phoenix Coyotes on March 30, 2006, and wore the "A" whenever McCauley was out of the line-up for the remainder of the season. Tallying 92 points in 58 games with the Sharks after the trade, Thornton finished the season with a league-leading 96 assists and 125 points total to earn the Art Ross Trophy as the league's top scorer. He became the first player to win the award while splitting the season between two teams. Due to Thornton's success, Cheechoo also enjoyed a career-season, winning the Rocket Richard Trophy as the NHL's top goal-scorer with 56 goals. However, in the 2006 playoffs, Thornton was once again criticized for his play, as his production decreased to 2 goals and 9 points in 11 games as the Sharks were ousted in the second round. In the off-season, Thornton was honoured for his regular season play and was awarded the Hart Memorial Trophy as the league' regular season MVP to go with his Art Ross Trophy. He is the only player in NHL history to win the Hart Trophy while playing for two different teams in the same season.