The team began play in 1985 as the Clearwater Phillies and were named for their Major League Baseball affiliate.

[5] The Clearwater Phillies began play in 1985 after the Philadelphia Phillies ended their affiliation with their High Class A minor league team, the Carolina League Peninsula Pilots, based in Hampton, Virginia, and placed their new team at Jack Russell Stadium.

With the move to the new ballpark, the Clearwater Phillies were renamed the "Threshers" and adopted a new team logo and colors.

In 2004, the Clearwater Threshers were managed by former Phillies player and Hall of Famer, Mike Schmidt.

Ernie Whitt was named the manager for the 2009 season after Shines was promoted to base coach for the New York Mets.

[8] On July 26, 2009, Pedro Martínez made a rehab start for the Threshers against the St. Lucie Mets at Spectrum Field.

Martinez pitched 11⁄3 innings before rain caused the game to be canceled, wiping out the official record of his start.