Independence is at the intersection of Farm roads 390 and 50, twelve miles northeast of Brenham in northeast Washington County. It was founded in 1835 by J. G. W. Pierson, Robert Stevenson, Colbert Baker, and Amasa F. Burchard on seventy-eight acres in Austin's colony on a part of the league of land granted by the Mexican government to Thomas S. Saul, who in turn granted it to Pierson and Baker. The community prospered and became a significant religious and educational center for the Republic of Texas. Frances Trask (see THOMPSON, FRANCES JUDITH SOMES TRASK) of Gloucester, Massachusetts, opened a boarding school for girls in 1835. In 1839 elders Thomas W. Cox and Thomas Spraggins organized the Independence Baptist Church, the fourth Missionary Baptist church formed in Texas; Cox was the first pastor. In the 1990s the church remained an active congregation, the second-oldest church affiliated with the Baptist General Convention of Texas. Sam Houston was a member of the church and was baptized in 1854 in Little Rocky Creek, two miles to the southeast.
In 1845 the Union Baptist Association, through its Texas Baptist Educational Society, acquired a charter to establish a university. Several towns made competitive bids, but Independence, then the wealthiest community in Texas, secured the institution. In 1846 Baylor University began operation as a coeducational school with twenty-four pupils at Independence. A post office was also established in Independence that year. In 1851 the school was divided into male and female departments, officially designated Baylor Female College and Baylor University in 1866. By the 1850s the town also had a hotel, a stagecoach depot, a jail, a Masonic lodge, a cemetery, and a small commercial district. In 1852 Independence was incorporated, with T. T. Clay as the first mayor. The Santa Fe railroad wanted to serve Independence, but the city fathers and Baylor administrators refused to grant the right-of-way. By the 1880s most of the railway lines in the area had bypassed Independence, and much of the trade was going to competing towns. Because college students had difficulty getting transportation to the Independence schools, officials decided in 1885 to move Baylor Female College (now the University of Mary Hardin-Baylor) to Belton and Baylor University to Waco, a move which marked the beginning of a century-long decline for Independence. By 1966 the population was 200, and the post office had been discontinued. In 1990 Independence was a rural settlement with a population of 140. That figure remained constant in 2000. Its numerous points of historical interest included the Independence Baptist Church, the Texas Baptist Historical Center, the home of Judge Coles, and Baylor College Park. Other interesting sites are the Old Independence Cemetery, where Judge Coles, Sam Houston, Jr., Moses Austin Bryan, T. T. Clay, and other prominent Texas citizens are buried, and the Margaret Houston House and Houston-Lea Family Cemetery, where Margaret M. L. Houston and her mother are interred.