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Flowery Branch lies in what was once Cherokee territory, with Indigenous trails and early trading posts predating European settlement. The area along the stream which would lend its name to the town was settled by English-speaking migrants in the early 19th century, farming the land and building roads. After removal of Native Americans in the 1830s, settlers expanded, establishing homesteads, churches, and small farms across the rolling terrain that borders the foothills of the Blue Ridge.

In 1874, the railroad (Richmond and Danville Air-Line) built a line through the area, connecting Charlotte to Atlanta, and Flowery Branch was formally established shortly thereafter as a railroad stop. This transformed the community: it became a hub for shipping cotton, agricultural goods, and later locally made furniture and leather goods. The train depot became central to town life, facilitating commerce and increasing population.

Infrastructure improvements over time included street development, road paving, bridges over streams, and the introduction of utilities like water, electricity, and telephone service. Later, with the creation of Lake Lanier nearby, waterfront development and improved highways boosted connectivity. Historic structures such as the old train depot and historic downtown buildings were preserved, some repurposed, contributing to the town's character.

The community of Flowery Branch has evolved through waves of growth, influenced by its proximity to Gainesville and Atlanta. As population increased in the late 20th and early 21st century, residential subdivisions expanded. Cultural institutions, schools, parks, and local businesses grew in number. Local residents take pride in heritage, hosting historic preservation, downtown revitalization, and events that highlight old-town charm.

Today Flowery Branch is a desirable suburban/ small-town blend. Many residents are commuters who enjoy access to Atlanta via highways and road networks, while preferring the more relaxed, scenic setting. The amenities include restaurants, shops, parks, and community services, and the historic downtown draws visitors. For homeowners, Flowery Branch offers strong appeal: natural beauty, community identity, and a balance of modern infrastructure with historic charm.