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Yellow Fever raged through much of Florida in the spring of 1888, after the mayor of Tampa announced that the disease was present in his city. Alachua County placed guards at all rail and road entrances to the county, and an officer at the county line had authority to put off the train anyone without a health card or certificate. Nevertheless, Yellow Jack spread, reaching Jacksonville in July, then hitting Fernandina about August. In Fernandina, officials denied yellow fever was present, then called for state help when commerce stopped and looting began.

He repeatedly denied yellow fever was in Fernandina, and so the Gainesville Guards were ordered to the stricken city. The guards, singing "We'll Hang the Yellow Jack to a Sour Apple Tree" boarded the Seaboard train for Waldo and Fernandina. Several guards died of yellow fever.

Then, in September, yellow fever was declared epidemic in Gainesville. Fear was widespread, and families fled the city before a quarantine was set up and the county line sealed. No one will ever know how many persons died in Gainesville; many were buried in mass graves, and few records were kept. The attached drawing is from a 1930's edition of the Atlanta Journal, in which the story was told of an Alachua County family which fled into Georgia, and their problems in passing across state lines.