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The county was founded December 8, 1857, and organized the next year. It is named after Barnard E. Bee, Sr., a secretary of state of the Republic of Texas.
During the Anglo-American land speculation of the 1830s, the area's earliest settlers were mainly Irish immigrants, but by the late 1840s and early 1850s, the rise of Jacksonian expansionism inspired Southern whites from the North Carolina, South Carolina, Louisiana, and Mississippi to occupy and build settlements in the area.
As the constitution of the Republic of Texas no longer recognized the Catholic Church (or any church) as the state religion and slave-holding settlers came to dominate the area in the 1840s, small Methodist, Presbyterian, and Baptist congregations began forming with sustained missionary support from these denominations. Research suggests that Baptists and Methodists comprised 65% of all Texas congregations by 1870.