One of the main points Du Bois is developing throughout his book is that, to quote him directly, “the defining problem of the 20th century [was] the color line.”
He continues to develop this point in chapter two, which he begins this way:
The problem of the twentieth century is the problem of the color-line,—the relation of the darker to the lighter races of men in Asia and Africa, in America and the islands of the sea. It was a phase of this problem that caused the Civil War; and however much they who marched South and North in 1861 may have fixed on the technical points, of union and local autonomy as a shibboleth, all nevertheless knew, as we know, that the question of Negro slavery was the real cause of the conflict. Curious it was, too, how this deeper question ever forced itself to the surface despite effort and disclaimer. No sooner had Northern armies touched Southern soil than this old question, newly guised, sprang from the earth,—What shall be done with Negroes? Peremptory military commands this way and that, could not answer the query; the Emancipation Proclamation seemed but to broaden and intensify the difficulties; and the War Amendments made the Negro problems of to-day.
Two things should be noted here.
Source: Blogging Through W. E. B. Du Bois: The Souls of Black Folk–Chapter 2