Cantera Venados FC

The club originally emerged in 1988 as Venados de Yucatán, when Jorge Arana Palma, acquired the Alacranes Rojos de Apatzingán franchise from the Segunda División de México and relocated it to Mérida, Yucatán, and it was during this stage when the colors that would identify them to this day are defined, green, yellow and white. During this first season, they were runners-up in the Segunda División de México in the 1988-89 season.

The club was renamed as Club Deportivo Atlético Yucatán in 1997, it played in the Primera División 'A' de México. The franchise was dissolved in 2001, but it returned the following year. The club won the title in the Invierno 1998 tournament, defeating Chivas Tijuana 1–0 in Mérida, and also played the Campeón de Ascenso 1999 against Unión de Curtidores, but lost 7–1.

Atlético Yucatán was renamed as Mérida Fútbol Club in 2003 by the brothers Arturo and Mauricio Millet Reyes, who obtained the Nacional de Tijuana franchise and relocated to Mérida, Yucatán.

After the Clausura 2005 tournament, the Millet brothers announced that they would be selling and relocating the team to Irapuato, Guanajuato renaming it Club Irapuato due to financial and 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 de México 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 de México.

On June 16, 2008, Arturo Millet Reyes announced that he had acquired the filial team of Monarcas 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 de México, that the team would remain in Mérida.

On November 11, 2008, the Federación Mexicana de Fútbol Asociación (FMF) granted the club the certification required to be promoted to the Primera División de México.

In the Clausura 2009, Mérida defeated Club Tijuana 1–0 on aggregate to win the Clausura title. Mérida lost the subsequent promotion play-off for the Primera División de México, after a defeat by Querétaro on penalties.

On December 4, 2010, the brothers Arturo and Mauricio Millet Reyes announced that Mérida F.C. would no longer form part of the Liga de Ascenso de México and that Monarcas Morelia would decide if a team would stay in the city, but that talks were also underway with Atlante 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 (Atlante UTN) swapped franchises to become the subsidiary team for Morelia. The franchise would later be transferred to Ciudad Nezahualcóyotl, State of Mexico and renamed Toros Neza.

The Federación Mexicana de Fútbol Asociación announced that the Apertura 2015 tournament would be 16 teams who would play the Ascenso MX instead of 14, as it was in recent tournaments. In addition, two clubs would be changing cities and states to the next season.

Estudiantes de Altamira became Cafetaleros de Tapachula, who were headquartered at the Estadio Olímpico in Tapachula, Chiapas; while Club Irapuato became Murcielagos F.C. and changed their headquarters to the Estadio Centenario located in Los Mochis, Sinaloa.

In addition to these changes, two new franchises were added later, that of Cimarrones de Sonora, headquartered at the Estadio Heroes de Nacozari in Hermosillo, Sonora, and the FC Juárez franchise began playing in the Estadio Olímpico Benito Juárez in Ciudad Juárez, Chihuahua.

Finally, it was announced that Mérida Fútbol Club would now be changing logo and be renamed Venados F.C. (keeping the venue in Mérida).

This meant that the Venados F.C. team would be the "rebirth" of Venados de Yucatán franchise in 2015.