He tendered his services to Mr.Lincoln, who at once commissioned him Colonel, and told him to take care of the frontier, as the regulars there had to come East to fight Jeff Davis.
Kit straightway proceeded to raise the First Regiment of New Mexico Volunteers, in which he had little difficulty, as the New Mexicans knew him well, and had the utmost confidence in him.

With these, during the war, he was busy fighting hostile Indians, and keeping others friendly, and in his famous campaign against the Navajos, in New Mexico, with only six hundred frontier volunteers captured some nine thousand prisoners.
The Indians withdrew into a wild canyon, where no white man, it was said, had ever penetrated, and believed to be impregnable.

But Kit pursued them from either end, and attacked them with pure Indian strategy and tactics; and the Navajos finding themselves thus surrounded, and their supplies cut off, outwitted by a keener fighter than themselves, surrendered at discretion.

Then he did not slaughter them, but marched them to a goodly reservation, and put them to work herding and planting, and they had continued peaceable ever since.
"Kit seemed thoroughly familiar with Indian life and character, and it must be conceded, that no American of his time knew our aborigines better--if any so well.

It must be set down to their credit, that he was their stout friend--no Boston philanthropist more so.