A day after scoring his 614th career goal for Barcelona, Messi reclaimed the trophy he last won in 2015.
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Liverpool defender Virgil van Dijk was second in the polling, followed by Cristiano Ronaldo, who shared the record of five Ballon d'Ors with Messi until Monday.
Messi's and Ronaldo's 10-year grip on the prestigious individual award organized by France Football magazine was ended last year by Luka Modric.
But Messi was back on top of his game over the past 12 months. Messi scored 36 times last season en route to the Spanish Liga title, and was the Champions League top scorer.
The Argentine has not showed any sign of slowing down since the start of the new European season, marking his 700th game for Barcelona last week with a goal and two assists in beating Borussia Dortmund 3-1.
Van Dijk clinched the 2019 Champions League crown with the Reds after defeating Messi's Barcelona in the semifinals 4-3 on aggregate, included a 4-0 win at Anfield in the return match.
Messi also won his sixth FIFA award in September, edging Van Dijk, who missed the chance to become the first defender to top the France Football poll since Italy's World Cup-winning captain, Fabio Cannavaro, in 2006.
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The Liverpool center back was among seven teammates nominated, along with goalkeeper Alisson Becker, defender Trent Alexander-Arnold, midfielder Georginio Wijnaldum and forwards Mohamed Salah, Sadio Mane and Roberto Firmino.
Rapinoe won the women's Ballon d'Or for leading the United States to World Cup glory in July.
She scored six goals in the championship, earning her the Golden Boot as the top scorer and the Golden Ball as the top player.
France Football magazine has been awarding the Ballon d'Or since 1956 and created a women's award for the first time last year when Norway's Ada Hegerberg won it. Hegerberg was fourth this time.
Juventus defender Mattis De Light won the Kopa Trophy for the best under-21 player, and the inaugural Yashin Trophy given to the year's best men's goalkeeper went to Liverpool's Alisson.