Originally, the main line deviated from its current route to serve East Palatka on the St. Johns River. The line ran from St. Augustine southwest to East Palatka, then turned southeast to Bunnell. In 1925, the Moultrie Cutoff was built from St. Augustine directly south to Bunnell to bypass East Palatka. Track to East Palatka remained in service but was downgraded to branch status and is now largely abandoned. The milepost numbers on the main line still reflect the original route, causing the mileposts to abruptly jump from 65 to 88 in Bunnell.