Although not an area of heavy settlement by stationary tribes such as the Puebloans, the Mora Valley was often used by nomadic nations, including the Ute, Navajo, and Apache.

[citation needed] Hispano settlers had occupied lands within the Mora Valley without legal title since Governor Juan Bautista de Anza of Nuevo México (then under the authority of the Spanish Empire) made peace with the Comanches in the late 18th century, opening up the east side of the Sangre de Cristo Mountains for settlement.

The written history of the settlement of Mora dates to Christian missionary church building in 1818,[3] three years before Mexican independence from Spain.

The creation of the Mora Land Grant by the Mexican government of New Mexico in 1835 began the legal and extensive settlement of the county.

[4] The settlers came primarily from Las Trampas, but also from Picuris and Embudo,[5] then from Santa Cruz de La Cañada, Taos, and the Ojo Caliente area, and later still from the southern part of New Mexico, moving on from the San Miguel del Vado Land Grant, and also coming in via Las Vegas, New Mexico.

The town of Mora was raided unsuccessfully in 1843 by a group of freebooters from the more narrowly defined Republic of Texas, on the pretext of stopping cattle rustling, but with a clear intent of horse theft and taking the local women and children as slaves.

During the Mexican–American War, beginning on April 25, 1846, much of New Mexico including Mora County was subject to the military occupation of United States under martial law.

During the Taos Revolt of the war, Mexican nationalist Hispano and Puebloan militia fought the United States Army, repelling a small force in the First Battle of Mora on January 24, 1847, only to endure the village and surrounding ranches, farms, and crops being burned to the ground in the Second Battle of Mora on February 1, effectively ending active rebellion in the area.

The Mexican–American War ended February 3, 1848, with Mora Valley and rest of the region then under formal US control, as the Mexican Cession of the Treaty of Guadalupe Hidalgo relinquished all claims by Mexico to lands north of the Rio Grande.

Still claimed by state of Texas until the Compromise of 1850, the New Mexico Territory, with smaller boundaries, was formalized on September 9 of that year.

This led to a protracted legal controversy, reaching all the way to the General Land Office, the Secretary of War, and the US Congress;[7] Nevertheless, the nearby fort and its garrison provided a stable source of income to local farmers, and several grist mills were founded in Mora, including a successful one opened in 1855 by regional trader and Taos Revolt US volunteer cavalry veteran Ceran St. Vrain.

The Mora Grant / Fort Union land dispute was exacerbated in 1868 by an order of President Andrew Johnson that established a government timber reservation that encompassed 53 more square miles the private grant land (the entire Turkey Mountains subrange of the Sangre de Cristos).

After being rebuilt twice, the fort eventually closed in 1891, still without restitution to land owners, despite the Kearny Code, Hidalgo Treaty, and other agreements supposedly guaranteeing continuity of Spanish and Mexican land-grant rights.

On February 21, 1916, Special Master William E. Gortner sold off unallotted common lands of the Mora Grant to the State Investment Company and Edward B. Wheeler in an auction at the door of the San Miguel County Courthouse.