Mérida F.C. was founded in 2003 by the brothers Arturo and Mauricio Millet Reyes, who obtained the franchise of Nacional de Tijuana.
Loss of franchise in 2005 and continuation at lower levels
After the Clausura 2005 tournament, the Millet brothers announced that they would be selling the team to Irapuato FC due to economic problems, citing lackluster attendance and poor support from the local government. Nevertheless, the brothers formed a team that participated in an amateur league in Yucatán and also opened a training facility in Argentina to scout local talent. Mérida F.C. returned to the professional ranks when they participated in the Tercera División in 2006/07. During 2007, the brothers oversaw the construction of a training facility located at the Unidad Deportiva Tamanché. By the 2007/08 season Mérida was participating in the Segunda División.
On June 16, 2008, Arturo Millet Reyes announced that he had acquired the filial team of Morelia. Millet Reyes has stated that his intention is to maintain the team in Mérida for an extended period of time, unlike in previous years. He also received a guarantee that if the Venados were to be promoted to the Primera División that the team would remain in Mérida. On November 11, 2008, the Federación Mexicana de Fútbol Asociación granted the club the certification required to be promoted to the Primera División. In the Clausura 2009 season Mérida defeated Club Tijuana 1–0 on aggregate to win the Clausura title. Mérida lost the subsequent promotion play-off for the Primera Division de Mexico, after a defeat by Querétaro FC on penalties.
Sale of franchise to Atlante
On 4 December 2010 the brothers Arturo and Mauricio Millet Reyes announced that Mérida F.C. would no longer form part of the Liga de Ascenso and that Monarcas Morelia would decide if a team would stay in the city, but that talks were also underway with Atlante F.C. regarding the creation of a link with them. The Mérida franchise was subsequently sold to Atlante and they became that team's filial team for the Clausura 2011, whilst the original Atlante filial team swapped franchises to become the subsidiary team for Morelia.
The Mexican Football Federation said the Apertura 2015 tournament will be 16 teams who play the Ascenso MX instead of 14, as it was in recent tournaments. In addition, two clubs change city and state to the next season. Estudiantes de Altamira will become Cafetaleros of Tapachula, whose headquarters will be the Olympic Stadium in Tapachula, in Chiapas; while Irapuato become Murcielagos FC and will play in Los Mochis, Sinaloa at the Estadio Centenario. In addition to these changes, there will be two new franchises, that of Cimarrones de Sonora, located in Heroes de Nacozari Stadium de Hermosillo. As the FC Juárez will use Benito Juarez Olympic Stadium. Finally, FC Mérida now be changing logo and will be called Venados FC. This could mean that the Venados FC team is the "rebirth" of Venados de Yucatán franchise.
Atlético Yucatán was a Mexican football club based in Mérida, Yucatán, México. The club played in the Primera A for most of their existence. The club was founded in 1988 the same year it joined the Segunda División Profesional. In their first years in 1988–89, the club would reach the finals against Potros Neza. The clubs tied in the first two games 2–2. Neza would come out with a 3–0 victory in the third match. In 1998 the club reached the final against Chivas Tijuana, where the club won 1–0 in Mérida. In 1999, the club played their promotion match against Unión de Curtidores but lost 7–1. ;Honors
