The next day, Baylor led his battalion across the Rio Grande into Mesilla, which sat at the crossroads of the two most traveled trails in the Southwest, the north-south El Camino Real de Tierra Adentro ("the Royal Road of the Interior Land") and the east-west Butterfield overland mail route.

On July 25, leaving a small force behind to guard the fort, Lynde led 380 Regulars to the village to drive out Baylor.

When Baylor refused, Lynde deployed his men into a skirmish line and opened fire with his mountain howitzers.

Lynde reformed his command but decided to retreat back to the fort, with the Confederates troops and armed Arizona citizens in pursuit.

Many Union troops apparently had filled their canteens with the fort's medicinal whiskey instead of water, hardly wise for a summertime march across desert country.

Baylor's success at Mesilla led to Henry Hopkins Sibley's ambitious New Mexico Campaign the following February.

On 25 November 1861 Major Lynde was, by direction of the President of the United States, Abraham Lincoln, dropped from the Army rolls for "abandoning his post — Fort Fillmore, N. Mex.