Though the area has been settled for some time, Marathon is a relatively new city, incorporated in 1999. The city set its boundaries "from the East end of the Seven Mile Bridge to the West end of Toms Harbors Bridge".
Among the islands found within the city limits Marathon include Boot Key, Knight Key, Hog Key, Vaca Key, Stirrup Key, Crawl Key, Little Crawl Key, East and West Sister’s Island, Deer Key, Fat Deer Key, Long Point Key, and Grassy Key.
The name Marathon dates back to the origin of the Florida East Coast Railroad. The name came about by the railroad workers who were working night and day to complete the railway – due to the unrelenting pace and struggle to complete the project, many of the workers complained that “this [the project] is getting to be a real Marathon”, and was later used to name the local station along the railroad.
As of the censusGR2 of 2000, there were 10,255 people, 4,597 households, and 2,735 families residing in the city. The population density was 457.7/km² (1,186.1/mi²). There were 6,791 housing units at an average density of 303.1/km² (785.4/mi²).
There were 4,597 households out of which 20.8% had children under the age of 18 living with them, 48.0% were married couples living together, 7.5% had a female householder with no husband present, and 40.5% were non-families. 29.2% of all households were made up of individuals and 8.6% had someone living alone who was 65 years of age or older. The average household size was 2.19 and the average family size was 2.68.
In the city the population was spread out with 17.3% under the age of 18, 6.1% from 18 to 24, 28.6% from 25 to 44, 32.0% from 45 to 64, and 16.0% who were 65 years of age or older. The median age was 44 years. For every 100 females there were 110.6 males. For every 100 females age 18 and over, there were 111.7 males.
The median income for a household in the city was $36,010, and the median income for a family was $46,361. Males had a median income of $27,057 versus $24,592 for females. The per capita income for the city was $22,894. About 9.4% of families and 14.2% of the population were below the poverty line, including 10.9% of those under age 18 and 13.5% of those age 65 or over.