Onate was replaced by Pedro de Peralta who moved the capital to the site of present-day Santa Fe. He named it San Francisco de la Santa Fe. Peralta was to rule for only 2 years; indeed, New Mexico would have no less than 22 governors between 1598 and 1680.
By 1617, the colony of New Mexico was in trouble. The Spaniards were beset by Navahos from the west and Apaches from the east and south. A series of ineffectual governors didn't help the situation. In 1637, Luis de Rosas became civil governor of New Mexico. His ruthless oppression of the Pueblo Indians resulted in a mass exodus of Indians to El Cuartelejo and to the Navaho lands. (The Navaho ultimately benefited from this influx of Pueblo Indians as they learned many of their lapidary and weaving skills from them!)
Hostilities between the Spaniards and Indians increased throughout the 17th Century. A severe drought from 1664 to 1679 only exacerbated the situation. As a result of the drought, the Navaho and Apache Indians increased their raids on both the Spanish colonies and Pueblo Indians. It was during this period of time that the peaceful Piro Indians were wiped out by the Apaches. Relations between the Spaniards and Pueblo Indians were no better. In 1675, a rebellion of Pueblo Indians resulted in the jailing of 47 Pueblo headmen. One of the headmen, Pope, was destined to lead the great Pueblo Uprising of 1680. Rumors of rebellion eventually stirred the new governor Antonio de Otermin to action, but for many of the colonists he acted too late. Nearly 400 Spaniards died during the first few days of the revolt. The survivors concentrated in Santa Fe and Isleta Pueblo where they were besieged by the Pueblo Indians. Otermin eventually broke the siege at Santa Fe, and then rescued the Spaniards at Isleta Pueblo. He then retreated south to Old Mexico, abandoning the colony founded by Juan de Onate 82 years before. In 1681, Otermin made an attempt to retake the upper Rio Grande provinces by marching north with 286 soldiers and Indian auxiliaries. Although he captured Isleta Pueblo without firing a shot, he was forced to withdraw south to Old Mexico again. It would be nearly a decade before another Spaniard would enter the upper Rio Grande area.
The Pueblo alliance proved to be very short-lived. After the departure of the Spaniards the traditional enmities that existed between the Pueblos began to surface. When Diego de Vargas Lujan Ponce de Leon was appointed governor of New Mexico in 1690, the upper Rio Grande area was ripe for the taking. Vargas was a strong advocate for the reconquest of New Mexico. Eventually, his superiors in Mexico City agreed to supply him with reinforcements and in 1692, he was ready to begin. (The Spaniards were further motivated by legends of a fabulously rich quicksilver mine in the Sierra Azul [Blue Mountains] of New Mexico, said to be located in the land of the Moquis). Vargas encountered no opposition as he advanced up the Rio Grande River. Santa Fe fell without a struggle, as did other important pueblos in the province. As John Upton Terrell noted in his landmark book “Pueblos, Gods, and Spaniards”, not a single drop of blood was shed in the upper Rio Grande area. Vargas returned to Old Mexico in late 1692. On his return the next year, he found that the situation on the upper Rio Grande had changed again. The rebellious Pueblo Indians had again risen in his absence. Vargas was forced to fight for Santa Fe and on December 30, 1693, the city again passed into Spanish hands. Further west, the Spaniards were unable to affect a surrender from the Hopis until 1696. It was while visiting the Hopi villages that Vargas encountered a metallic, orange-colored substance that was used by the Hopi to remove blemishes on the skin. This cinnabar-like substance left a purplish luster on the skin and was greasy. The Spaniards must have been thinking of the legendary Sierra Azul quicksilver mines as they collected samples of the material for assaying. (To their eventual disappointment, no mercury was found in the samples.)
After the reconquest of New Mexico in 1693, the Spanish hold on the American Southwest appeared to be secure. But in 1706, Captain Juan de Ulibarri encountered unsettling evidence of French encroachment on Spanish territory. While pursuing some Picuries who had fled from the Spanish in 1696, Ulibarri came across a new French rifle at El Cuartelejo (near present-day Las Animas, Colorado). Spanish fears of French incursions were not unfounded. In 1682, LaSalle had claimed the Mississippi Valley for France. In 1689, a Spanish expedition to Matagordo Bay on the Texas coast came across the remnants of a French colony established by LaSalle on Garcitas Creek. In 1714, the Frenchman Juchereau de St. Denis was caught trespassing in Spanish territory. Five years later, in 1719, Claude du Tisne journeyed west into central Kansas while Benard de la Harpe made his way up the Red River almost to the site of present-day Tulsa, Oklahoma.
In that same year, the governor of New Mexico, Antonio de Valverde, while on an expedition in southeastern Colorado, heard rumors of French settlements to the east. In 1720, Valverde dispatched an expeditionary force under Pedro de Villasur eastward onto the plains to search for signs of invading Frenchmen. This ill-fated expedition was surprised by Pawnee and Otoe Indians on the Platte River and nearly wiped out.
The early 1700's also witnessed the appearance of a ferocious new tribe of Indians from the north. This migration was to have a significant effect on the Spanish colonies in New Mexico. The invading Comanche Indians began to enter the area by 1705, driving the Plains Apache from their traditional homeland. But the Comanches were not the only Indians the Spaniards had to worry about. The Faraon Apache had been raiding into southern and eastern New Mexico, as well as on the Rio Grande, for many years. In 1715, Governor Juan Ignacio Flores Mogollon was forced to retaliate by sending a military expedition led by Captain Juan Paez Hurtado against the Faraon Apaches. Accompanying the expedition was the notorious Frenchman Juan de L'Archeveque who had participated in the murder of LaSalle in 1687. (L'Archeveque was massacred along with Pedro de Villasur by Pawnees near the Platte River on August 15, 1720.) To his dismay, Hurtado was unable to find a single Faraon Apache during the entire expedition.
And then in 1739, the first French traders from Louisiana, Paul and Peter Mallet, reached Santa Fe. Shortly thereafter, the Comanche Indians began to raid Pecos and Galisteo pueblos, killing nearly 200 people in a five year period. The Spaniards in New Mexico began to suspect that the French were behind the Indian raids. In 1748, French deserters from a military post on the Arkansas River (Pierre Satren, Louis Febre, and Joseph Riballo) turned up in Santa Fe and were allowed to stay. But Spanish policy was about to change. In 1752, Jean Chapuis and Luis Feuilli were arrested by Spanish authorities along with eight other Frenchmen and marched off to Mexico. This state of affairs lasted until 1763 when the French ceased to be a threat to the Spaniards of New Mexico. It was in this year that Louisiana became Spanish territory.
Meanwhile, the unrelenting Comanche Indians began to increase their raids on Spanish holdings. In 1758, a horde of Comanches, Wichitas, and Caddoans descended upon the San Saba mission (near present-day Menard, Texas) and slaughtered all the inhabitants (including two missionaries, Fray Terreros and Fray Santiesteban). In 1760, the Taos Valley was raided. In 1768, the notorious Comanche chief Cuerno Verde (Green Horn) went on the warpath against the Spaniards, leading raids against Ojo Caliente, Taos, Pecos, Picuris, and Galisteo. In 1774, the Comanches began to intensify their raids against the upper Rio Grande pueblos. By 1777, the situation had become unbearable. At Tome Pueblo, south of Albuquerque, the Comanches killed 51 people. Raids also occurred at Valencia, Galisteo, and Isleta. In 1778, the Spanish governor, Don Juan Bautista de Anza, mounted an expedition against Cuerno Verde (Greenhorn), the most implacable of the Comanche chiefs. The Spaniards surprised Cuerno Verde at the base of Greenhorn Mountain (near Rye, Colorado) and decisively defeated him. In 1785, after 45 years of ceaseless raiding, the Comanche threat to the colonies was finally ended. During that year, the last hostile chief (White Bull) was eliminated, resulting in a peace treaty between the Spaniards and Comanches that would never be broken in New Mexico.
The acquisition of Louisiana by the Spanish in 1763 set the stage for the future Santa Fe Trail. In the period stretching from 1786 to 1793, Pierre Vial (a Frenchman employed by the governor of New Mexico) blazed a trail from Santa Fe to Natchitoches, Louisiana. But in 1800, under the secret treaty of San Ildefonso, the Louisiana territory reverted back to the French under Napoleon. Events were happening quickly now. In 1803, Napoleon sold Louisiana to the United States. It didn't take long for the first American traders to appear in New Mexico. In 1804, Baptiste Lalande and Jeannot Metoyer (agents of William Morrison from Kaskaskia, Illinois) arrived in Santa Fe with goods from Illinois. Lalande absconded with Morrison's goods and remained in Santa Fe. In 1805, mountain man James Purcell arrived in Santa Fe, found it to his liking, and stayed there 19 years. (James Purcell was probably the first white man to discover gold in Colorado). The following year, the famous explorer Zebulon Pike was caught trespassing on Spanish territory and was arrested. During his visit to New Mexico, Pike met with both Purcell and Lalande. In 1807, the old but hale Jacques Clamorgan (who was 74 years old at the time) arrived in Santa Fe with trade goods from St. Louis. Clamorgan had been a partner of Manuel Lisa in 1806, but Lisa had backed out of the Santa Fe expedition in favor of the Missouri River fur trade. Instead of giving up on the venture Clamorgan led the expedition himself.