The Mark Twain Project Online (MTPO) edition of Mark Twain's Mysterious Stranger Manuscripts reproduces the text of William M. Gibson's 1969 edition. Additional endnotes have been added to the MTPO edition. The paragraphs below explain the additional endnotes.

For his 1969 edition Gibson occasionally introduced extra white spaces between paragraphs in "The Chronicle of Young Satan," "Schoolhouse Hill," and "No. 44." Gibson provides no explanation of these extra white spaces in his endnotes. Because the three main texts in Gibson's edition are transcriptions of manuscripts in the Mark Twain Papers, the current editors checked the printed edition against the manuscripts. While consulting the manuscripts, the editors discovered that the extra white spaces Gibson introduced between paragraphs represent different types of divisions in the manuscripts. Gibson partially addresses the white spaces in the introduction to the textual apparatus of his edition (the "Textual Commentary"):

For instance, Gibson inserts extra white space between two paragraphs on page 74 of his edition. This white space represents a page break between "Chronicle" manuscript pages 117 and 118. A similar page break occurs between manuscript pages 178 and 179. Gibson interprets this break in the manuscript as the beginning of "Chapter 5" and inserts a chapter heading (Gibson's, not Twain's) on page 94 of his edition. As he never explains his rationale for representing the same or similar manuscript page breaks differently, the current editors decided to provide endnotes describing the extra white spaces that Gibson implements without further remark. Users of the MTPO edition therefore have the opportunity to consider why Gibson inserted chapters in some instances and extra white spaces in others. This effort yielded thirteen additional endnotes, classified as "textual notes," in the 2019 MTPO edition. Among the thirteen notes, the user will see that nine describe white spaces in the printed text of "Chronicle," one describes a white space in "Schoolhouse Hill," and three describe white spaces in "No. 44." None of these instances and thus none of the differences between them are recorded in the 1969 edition's apparatus.

Additionally, the MTPO edition of Mysterious Stranger Manuscripts incorporates corrections made to Gibson's edition by MTP editors after its 1969 publication. These corrections come from a hand-emended volume held in the Mark Twain Project's library; they exclusively address corrections to the 1969 edition's textual apparatus. The hand-emended volume yielded two new endnotes: 1) an editorial emendation of the word "ley" to "lye" on page 259; 2) a textual note for the emended word "saccharin" on page 330. As with the other new endnotes, the incorporation of these corrections are distinguished from the original edition's apparatus entries with the heading: "MTPO Note." Other corrections from the hand-emended copy have been added without the "MTPO Note" heading: 1) a clarification regarding the editorial emendation at 298.4, which states that the emendation is Mark Twain's own hand correction in the typescript; 2) a clarification regarding the editorial emendation at 330.12 that it is in the text of the typescript; and 3) a clarification about the dating of ink in the textual note at 320.23.

Lastly, the MTPO edition of Mysterious Stranger Manuscripts demanded six endnotes (again classified as "textual notes") pertaining to "Appendix B: Working Notes and Related Matter." These notes describe three instances where Twain used brackets to group together multiple entries in lists of character names. These additions are also distinguished from the 1969 notes with the "MTPO Note" heading.

MS      Manuscript
MT      Mark Twain
MTP      Mark Twain Papers, The Bancroft Library, University of California, Berkeley
TS      Typescript
DE, XXVII      The Mysterious Stranger and Other Stories, “Definitive Edition” (New York, 1923), XXVII
Europe       Europe and Elsewhere (New York, 1923)
Hadleyburg       The Man That Corrupted Hadleyburg and Other Stories and Essays (New York, 1900)
HH&T       Hannibal, Huck & Tom, ed. Walter Blair (Berkeley and Los Angeles, 1969)
MTA       Mark Twain's Autobiography, ed. Albert Bigelow Paine (New York, 1924)
MTB       Albert Bigelow Paine, Mark Twain: A Biography (New York, 1912)
MTHL       Mark Twain–Howells Letters, ed. Henry Nash Smith and William M. Gibson (Cambridge, Massachusetts, 1960)
MTL       Mark Twain's Letters, ed. Albert Bigelow Paine (New York, 1917)
MTN       Mark Twain's Notebook, ed. Albert Bigelow Paine (New York, 1935)
MTSatan       John S. Tuckey, Mark Twain and Little Satan, The Writing of The Mysterious Stranger (West Lafayette, Indiana, 1963)
MTTB       Mark Twain's Travels with Mr. Brown, ed. Franklin Walker and G. Ezra Dane (New York, 1940)
MTW       Bernard DeVoto, Mark Twain at Work (Cambridge, Massachusetts, 1942)
SCH       Dixon Wecter, Sam Clemens of Hannibal (Boston, 1952)
What Is Man?       What Is Man? and Other Essays (New York, 1917)
WWD       Mark Twain's Which Was the Dream?, ed. John S. Tuckey (Berkeley and Los Angeles, 1967)