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The Argentina captain beat off competition from last year’s winner Cristiano Ronaldo and Juventus goalkeeper Gianluigi Buffon to be named Best Player of the Year.
“Obviously I am very happy to be here and delighted to win this award but as always, the most important thing is the collective, the team,” Messi said after receiving the award on Sunday.
“It is difficult to pick out one moment from what has been an extraordinary year for Barca. The whole year has been wonderful.”
Following the victory, Messi will also be up against Ronaldo and his Barcelona team-mate Neymar for the FIFA Ballon d’Or on January 11.
Barcelona, who won an historic treble in 2014-15, were named Best Club of the Year, while their chief Josep Maria Bartomeu was awarded the Best President of the Year accolade.
“I am just one of Barcelona’s 140,000 club members and I am extremely proud to be their president,” said Bartomeu.
“But this award really belongs to our club members and the 39 presidents before me during the club’s 116-year history. I would also like to give special thanks to the players for all of the efforts they made this year.”
Belgium boss Marc Wilmots was named as Best Coach of the Year ahead of Barca’s Luis Enrique and Italy’s Antonio Conte after leading his country to top spot in the FIFA world rankings.
Elsewhere, New York City pair Andrea Pirlo and Frank Lampard were recognised and given Player Career Awards.
Jorge Mendes was handed the award for Best Agent of the Year, while Portuguese club Benfica were named as the Best Academy of the Year.