The emergence of germ theory during the nineteenth century transformed Western medicine. By the 1870s, public health officials in the American South used germ theory to promote sanitation efforts to control public health crises, such as yellow fever epidemics. Before the discovery of mosquito transmission of yellow fever, physicians of the late nineteenth century believed the disease was spread by a highly contagious germ. Prominent medical practitioners of New Orleans, such as Confederate Army veteran Dr. Joseph Jones, used available scientific knowledge and investigation to attempt to control yellow fever during the Reconstruction period, a period rife with political and racial tension in New Orleans. This paper will analyze nineteenth century Southern medicine through the work of Dr. Joseph Jones and will argue that despite the use of cutting edge scientific methods of the era, the political challenges of the Reconstruction period shaded the public health policies in New Orleans.