Beginning in 1877, when Reconstruction ended with the federal government withdrawing its troops from the South, Lynch wrote and published four books: these analyzed the political situation in the South during and after Reconstruction. He is best known for his book, "The Facts of Reconstruction" (1913). It is available online at the Gutenberg Project. In it, he argued against the prevailing view of the Dunning School, conservative white historians who downplayed African-American contributions and the achievements of the Reconstruction era. Lynch emphasized how significant was the ratification of the 14th and 15th Amendments to the Constitution, which granted full citizenship to all persons without restriction of race or color, and suffrage to minority males.