The flag of Florida consists of a red saltire, St. Andrew's Cross, on a white background, with the state seal superimposed on the center. The design was approved by a popular referendum in 1900. The current design has been in use since 1985, after the state seal was graphically improved and officially sanctioned for use by state officials.
While both the modern Alabama and Florida state flags may have some historical tribute to Spanish rule in their design, both were definitely patterned after the battle flags of the Army of Northern Virginia (ANV)- under which the bulk of the troops from both states fought.
Both of these flags have documentation stating the influence of the ANV battle flags in their design - particularly the flag of Alabama - which was created under the administration of Governor William Oates. Oates was a former regimental commander in the ANV. He is most famous for leading the confederate assault on Little Round Top at the Battle of Gettysburg. [Text from FotW]
Shown below are various flags that have flown over what is now Florida.
Cross of Burgundy flag, flag of the Spanish Empire from the 16th to the 19th centuries.
The Spanish flag after 1785. Its colors are reflected in the present seal of Florida.
Florida's first state flag was adopted during the American Civil War. Design by Governor Perry.
A red roughly-pruned saltire (also known as St. Andrew's cross). Used as Spanish naval ensign from 1506 to 1701, and as battle flag up to 1843. It was specially used as insignia to Spanish Empire overseas viceroyalties - Florida was part of the Viceroyalty of New Spain. Its Spanish usage dates from the marriage between Philip I of Spain and Mary of Burgundy, when the king decided to honor the House of Burgundy, the royal house of his new mother-in-law.
Its origins are discussed: it can be firstly adopted by the Order of the Golden Fleece, in 1429, but, in the 1490s, the writer Pedro de Ayala claims it was adopted by a previous Duke of Burgundy in tribute to his Scottish soldiers.
In the designs, it can appear both as a roughly-pruned saltire or as a straight saltire (as it appears in current state flag).
Many designs use an orange circle, that can represent one or both of these symbols: the Sun or a orange. Florida state has tropical and subtropical climates, the reason it's named "The Sunshine State". The orange refers to the fact citrus fruit, especially oranges, are a major part of the state economy. Florida produces the majority of citrus fruit grown in the United States.
Sometimes, the orange disc is substituted by other depiction of the sun.