Thornton was the Bruins' leading scorer last season with 23 goals and 37 assists. Samsonov, a former NHL rookie of the year, was third on the team with 19 goals and 26 assists.
Anson Carter, the team's second leading scorer a year ago, is still unsigned.
The Bruins' holdout problems have attracted attention because of the hard line taken by general manager Harry Sinden.
Feeling that players missing camp was hurting them and the team, Sinden vowed this year to decrease his offer for every day the player is out. He insisted he wasn't fining players, but said a player's value decreased for having missed camp.
Thornton was the Bruins' first pick in the 1997 draft. He has improved each season in the league, and missed just two games to injuries over the last two years. Last season, he became the second player in club history to lead the team in goals, assists, points and penalty minutes in a season.
Samsonov and entering his fourth NHL season, was the eighth overall pick in the 1997 draft. He had 47 points in 81 games during his rookie campaign and a career high 51 points in 1998-99.
Terms of the deal were not made public.
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