Ron Hainsey notched a goal and a pair of helpers for the Thrashers, winners of four straight games, including a home-and-home weekend series with the Flyers.
With the victory, Atlanta moved within a point of Boston for the eighth and final playoff berth in the Eastern Conference.
Mike Richards got the only goal for the Flyers, who with the loss dropped their fourth game in five contests. Brian Boucher collected 28 saves in the loss.
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