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Unión Magdalena was founded as Deportivo Samarios on 10 March 1951. The team was founded with the help of José Eduardo Gnecco Correa and Eduardo Dávila Riascos and was formed by the squad of the Hungaria FbC Roma when it was disbanded after a tour in South America. The first team consisted in 10 Colombians, 8 Hungarians, 2 Yugoslavs, 1 Austrian, 1 Argentine, 1 Italian and 1 Romanian. Deportivo Samarios debuted on league that same year and placed 14th. That season, the team achieved the record of the biggest win in the Colombian league against Universidad, with a score of 12–1.

The club was re-founded as Unión Magdalena on 19 April 1953. Unión has only won one championship, in 1968 playing against Deportivo Cali in the final, thus becoming the first football club of the Caribbean region of Colombia to win a football championship in history. Carlos Valderrama, born in Santa Marta and one of the most famous Colombian footballer, started his career in this club.

Relegated in 2005 after losing 3–0 to Deportivo Pereira, Unión earned automatic promotion to the 2019 Categoría Primera A season, after playing 13 years in the second division football league. Despite qualifying for the semifinals of the 2019 Apertura, Unión's performance in the Finalización tournament was poor and the club ended up being relegated on 29 October after losing 3–1 to Once Caldas.

Red and blue stripes compose the traditional shirt of the team, and its design is inspired by the Argentine club San Lorenzo de Almagro.

2021 controversy and promotion

On 4 December 2021, the last matchday of the semi-final Group B of the second tournament of the 2021 Primera B season, Unión Magdalena sealed their promotion to Categoría Primera A after coming back from a 1–0 deficit against Llaneros in Villavicencio with a couple of goals in quick succession in stoppage time to win the game by a 2–1 score and get promoted at the expense of Fortaleza, who were clinching promotion with the score in Villavicencio despite losing their final match to Bogotá at the same time. However, video footage of Unión Magdalena's winning goal appeared to show the Llaneros players backing off and failing to make an effort to prevent their rivals from scoring. The events sparked outrage both within the country and abroad, with Colombian internationals Juan Cuadrado and Mateus Uribe expressing their displeasure, calling them "a lack of respect" and "an embarrassment for Colombian football", whilst President of Colombia Iván Duque Márquez stated it was a "national disgrace".

In response to the growing backlash, as well as calls from Fortaleza to get the match annulled and Unión Magdalena's promotion reversed, Dimayor chairman Fernando Jaramillo ordered the opening of an inquiry on the match events while also requesting the Office of the Attorney General of Colombia to investigate whether any criminal offenses had been committed, but on 7 December 2021, Jaramillo stated that the tournament would not be paused and Unión Magdalena's promotion would not be overturned while due process was completed. However, amid the ongoing inquiries, the Torneo II's final match between Cortuluá and Unión Magdalena, which was originally scheduled to be played on 11 December 2021 in Tuluá was postponed until further notice.

On 30 December 2021 Dimayor's disciplinary commission closed the investigation on Unión Magdalena as it found no evidence implying that members of the aforementioned club had been responsible for the events that occurred in the match against Llaneros, thus confirming their promotion to Primera A for the 2022 season.