Messi is one of three Barcelona players to have been named alongside team-mates Xavi and Andres Iniesta, while Real Madrid's Brazilian midfielder Kaka completes the line-up.
In the run-up to the 2010 World Cup, favourites Spain have two players, and Portugal, Brazil and Argentina one each. No English player has made the cut, nor has any player currently playing in the Premier League.
England striker Kelly Smith is up against Brazil's Cristiane and Marta and Germany's Inka Grings and Birgit Prinz for the women's award.
Two new awards have been introduced for 2009; the FIFA Puskas Award, and the FIFA/FIFPro World XI. The Puskas Award, created in honour of Hungarian legend Ferenc Puskas, will be awarded to the "most beautiful goal" during the year, while the World XI will name the best 11 players in the world, as voted for by professional players around the globe.
The winners will be announced on December 21 in Zurich.