[2] It was built by order of Mariano Guadalupe Vallejo to house the Mexican soldiers that had been transferred from the Presidio of San Francisco in 1835.

The Presidio Company and their commander, Vallejo, were also responsible for controlling the Native Americans living on the northern border of Mexican California.

[2] Throughout the Mexican–American War and the subsequent California Gold Rush these forces continued to confront Native Americans hostile to invaders occupying their lands.

California Governor Jose Figueroa had ordered the Company north from the Presidio of San Francisco as part of his plan to comply with instructions from the national government to establish a strong garrison in the region north of the San Francisco Bay to protect the area from encroachments of foreigners.

Vallejo's approach to controlling the border region combined direct military action, treaties with native groups, and by forming alliances with Indian leaders on the west (Chief Marin) and east (Chief Solano - who provided auxiliary men when the Company way fighting other Native groups).

Among his other reasons may have been avoiding being drawn into a rebellion against Governor Micheltorena by his nephew Juan Alvarado and childhood friend José Castro.

[13] They next determined to seize the Pueblo of Sonoma to deny the Californians a rallying point north of San Francisco Bay.

Captain John Charles Frémont and his mapping expedition group arrived in Sonoma on June 24, throwing off any pretense of neutrality.

[17] The next day Frémont, leaving the fifty men of Company B at the barracks, left with the rest of the Battalion for Sutter's Fort They took with them two of the captured field pieces as well as muskets, a supply of ammunition, blankets, horses, and cattle.

[18] Seven weeks after war with Mexico had been declared in Washington, D.C., Commodore John D. Sloat, commander of the U.S. Navy's Pacific Squadron, after being assured that war with Mexico had been declared, instructed the captains of his ships to occupy Monterey on July 7 and Yerba Buena (now San Francisco) on July 9.

Raising the Stars and Stripes in front of the barracks marked the end of the Bear Flag Revolt and the California Republic.

[7] Sonoma lost its military population in January, 1852, when the troops moved to Benicia and other assignments in California and Oregon.

Vallejo's two sons, Uladislao and Napoleon leased part of the building in 1872-73 for their winemaking operation in exchange for one quarter of the profits.

[22][4] On May 19, 1937, the Native Sons of the Golden West placed a bronze commemorative plaque in the adobe wall of the barracks, marking the building, erected in 1836, as the spot in which the Bear Flag was designed and made.