The Bonnie Blue was used by the Republic of Texas from 1836 to 1839. In 1861, it flew over the capital building in Jackson, Mississippi, inspiring the southern patriotic song - "The Bonnie Blue Flag," composed by Harry MaCarthy. It was also used in one form or another by numerous southern confederate states.
Stars and Bars
The white stars on the blue field represent the original Confederate States of Alabama, Florida, Georgia, Louisiana, Mississippi, South Carolina and Texas.
Stars and Bars (final version)
The thirteen stars represented the original seven Confederate States, as well as the states of Arkansas, North Carolina, Tennessee and Virginia. Note that Kentucky and Missouri each have a star, but efforts to secede from the Union within their individual states eventually failed. Regardless, the stars remained.
Confederate Battle Flag
Perhaps the most recognizable flag from the Civil War period was the Confederate Battle Flag (shown above). It was carried by Confederate troops throughout the war.
Confederate Navy Jack
Beginning in 1863, this flag was used at sea by the navy, and became (in many ways) the recognizable symbol of the southern states.