The name "Marathona" originates from the fennel herb called  "marathos" in Greek (def. "a place full of fennel"). Ancient Marathona occupied 4 points that were Marathona, Probalinthus, Tricorythus, and Oenoe, which originally formed the Tetrapolis, one of the 12 districts into where Attica was divided before the time of Theseus. Here is where, Xuthus, who married the daughter of Erechtheus, was said to have reigned. It is also here that the Heracleidae took refuge when driven out of Peloponnesus, and defeated Eurystheus. The Marathonii claimed to be the first people in Greece who paid divine honors to Heracles - who possessed a sanctuary in the area. The philosopher and aristocrat Herodes Atticus was also born in Marathona.

Marathona is also celebrated in the stories of Theseus, who conquered the ferocious bull that used to devastate the plain. Furthermore, Marathona is mentioned in Homer's Odyssey in a way that implies that it was then a place of importance. In mythology, its name was derived from an eponymous hero Marathon, who is described by Pausanias as a son of Epopeus, King of Sicyon, who fled to Attica as a consequence of the cruelty of his father.
 

Few places have obtained such celebrity in the history of the world as Marathona, on account of the victory the Athenians gained over the Persians in 490 B.C. (Battle of Marathon). After Miltiades (the General of the Greek forces) defeated Darius' forces, the Persians decided to sail from Marathona to Athens in order to pillage the unprotected city. Miltiades ordered all his hoplite forces to march "double time" back to Athens so that by the time Darius' troops arrived they found the same Greek force waiting for them. The victory further prevented Eastern despotism and preserved not only Greek but also European culture.

In 2011, the Municipality of Marathona was formed in Attica with the merger of the Municipalities of Nea Makri and Marathona, and the communities of Grammatiko and Barnabas. Marathona presents an exceptional natural landscape. It has the unique artificial lake of Attica, rich green, a fertile plain, and 12 km of sandy beach in the historic bay of Marathona. The municipality is Marathona has 28,000 residents.