The town of Conchagua was founded in 1543; and on July 12th in 1824 was annexed to the department of San Miguel, and on June 22nd in 1865 was declared as part of the department of La Union. On September 23, 1971, it obtained the title of village.
It was declared as city in 2001.
 

 The population of Conchagua is of Lenca origin, where the conchaguas or comixaguas originally lived in the islands of theFonseca's Gulf, more specifically in what is now known as "conchaguita island", they shared these lands with other tribe called "los tecas", In 1522 an expedition sent by Gil Gonzalez Dávila under the command of Andres Niño, discovered the Gulf of Fonseca with its islands Meanguera del Golfo which Andres Niño baptized with the name of "petronila" and conchaguita, for those times the natives of the islands were formed in a considerable amount of people; other peoples also existed on the mainland known as "Los Amapalas", whose support was in the place that is now known as an old town a few kilometers east of the city of La Union.

 Francis Drake, famous sailor and English privateer made several expeditions of piracy against the Spanish colonies of America between the years of 1570 and 1572. In 1582 Francis Drake led the violent invasion looting and murdering the inhabitants of the island of the Gulf, the invasion originated a mass exodus of the inhabitants of the island to the mainland, in such a way that the conchaguas were located in the environs of the port of Amapala; the divergences between the Amapalas and the Conchaguas arose almost immediately, becoming more and more accentuated.

​

The Amapalas prohibited the Conchaguas from using their jetty, which forced them to establish a new port provided in the Bay of the Union, known as: "Los embarcaderos de los Conchaguas" in the same place where today is the city of La Unión. According to this historical data, "El embarcadero de LosConchaguas" was the first formal site of settlement of the conchaguas, after emigrating from the Gulf Islands, such port offered better products and personnel than in some provinces of San Salvador and San Miguel set directed to Nicaragua.

 In the importance given to the new port by its proximity to the aforementioned provinces, gradually moved to the old port of Amapala, to extinguish it as such, as concequence  flourished Conchagua town; but for reasons not yet very clear it was soon eclipsed by the new municipality: San Carlos de La Union. "In autochthonous toponymy of the department of La Union" we find the following "The place where the new town of Conchagua was founded stopped offering the sources that came from drinking water to the population". Finally a public deed was obtained in the year of 1712 granted by the governor of arms Francisco Rodriguez Berríos.