The name Marathon dates back to the origin of the Florida East Coast Railroad.

The name came from the railroad workers who were working night and day to complete the railway; due to the unrelenting pace and struggle to complete the project, workers complained that "this is getting to be a real marathon", and the word was later used to name the local railroad station.

[6] The Keys historian Dan Gallager in his book Florida's Great Ocean Railway credits New York playwright Witter Bynner for naming Marathon.

According to Gallager, J.R. Parrott, then Florida East Coast Railway's President and General Manager, invited Brynner to the Keys to "plot stations for the railroad".

"[7] Marathon experienced significant damage from the September 10, 2017, U.S. landfall of Hurricane Irma.

[8] Marathon was one of the earliest spots in the Keys to receive transport of needed supplies to deal with the aftermath of Irma.

The Air National Guard landed two C-130 transport planes every two hours beginning on the morning of September 11.

To the south or southeast lies Hawk Channel, a popular passage for vessels traveling along the Keys.

As of 2000, English as a first language accounted for 78.10%, while Spanish as a mother tongue made up 20.95% of the population.

Bountiful reefs around Marathon make it a popular diving, snorkeling, spearfishing, and lobster tickling area.

The vicinity of the airport is one of the most reliable sites in the United States to see the hard-to-find Antillean nighthawk.

As in the rest of the Keys in summer, gray kingbirds are often seen on telephone wires along US 1 and black-whiskered vireos incessantly sing in the hammocks.

The Overseas Highway extends westward, connecting Marathon with Key West.