Letters by John Muir

The Life and Letters of John Muir, by William Frederic Badè (1924) - The full text of this two-volume book contains thousands of Muir's letters and previously unpublished writings, along with Badè's biography.
Letters to a Friend (1915) - Letters written by Muir to his mentor, Jeanne Carr.
Original manuscript letters of John Muir, 1861-1914, Wisconsin Historical Society (off-site link)
These 30 letters, totaling more than 100 pages, were written by Muir to five correspondents. Twenty are to his old friend Emily Pelton, with whose family he boarded in Prairie du Chien in 1860-61, or to her aunt Frances. Four other letters are to childhood friends from Wisconsin, James Whitehead and Milton Griswold. A few other letters of a routine business nature are also included. All but six of the letters have never been previously published in their entirety (though typed copies of most were included in Muir's manuscripts at the University of the Pacific).
Related Collections to the John Muir Papers - Letters are contained in various collections housed by the University of the Pacific, many digitized and available on the web. See especially the James Eastman Shone Collection, John Muir and Ina Coolbrith Correspondence 1906-1911, and the John Muir and William Trout Correspondence.
A Letter from John Muir to S. Hall Young, 1910 May 31 Introduced by Bruce Merrell
Victorians and Meadowlarks: Two Muir Letters Rediscovered
New Cache Of Muir Letters Discovered In England" by Ron Limbaugh