Bowl Championship Subdivision (formerly Division 1A)
There are 121 Universities with BCS football programs in 2007. These are the largest Universities.  The Division 1-A National Championship is currently awarded via the Bowl Championship Series system. 

BCS Universities in Florida are:

Florida Atlantic University
Florida International University
Florida State University
University of Central Florida
University of Florida
University of Miami
University of South Florida

Miami, Florida and Florida State have each won multiple National Championships.

Division I-AA: (also known as the "Football Championship Subdivision")
There are 120 Division I-AA Colleges/Universities with football programs in 2005.
These are divided into 15 conferences and a group of several independent colleges.

FCS teams in Florida:

Jacksonville University (Dolphins) -Pioneer Conference
Florida A&M  (Rattlers) - Mid Eastern Conference
Bethune-Cookman University (Wildcats) - Mid Eastern Conference

Division 1-AA teams in nearby states include:

Georgia: Savannah State University, Georgia Southern University.

South Carolina: Wofford College, Furman University, The Citadel, South Carolina State University, Coastal Carolina University, Charleston Southern University.

Alabama: Jacksonville State University, Samford University, Alabama A&M University, Alabama State University

Mississippi: Miss. Valley State University, Jackson State University, Alcorn State University

North Carolina: Gardner Webb University, NC A&T State University, Davidson College, Appalachian State University, Elon University, Western Carolina University, Western Carolina University.

Tennessee: University of Tennessee at Chattanooga, Austin Peay State University, University of Tennessee at Martin, Tennessee Technological University, Tennessee State University.

Kentucky: Western Kentucky University, Eastern Kentucky University, Murray State University, Morehead State University, 

Louisiana: McNeese State University, Nicholls State University, Northwestern State University, Southeastern Louisiana University, Grambling State University, Southern University-Baton Rouge, 

Virginia: James Madison University, University of Richmond, College of William and Mary, Liberty University, Virginia Military Institute (VMI), Hampton University, Norfolk State University.

FCS (formerly Div I-AA)  has a 16 team playoff for a National Championship.

Check the links below for info on the other divisions of college football.