Here is an interesting panel presentation given two months ago at the Southern Historical Association about ways to teach Reconstruction at the undergraduate level. There are very few courses that focus exclusively on Reconstruction.
The era is typically examined for three to six hours during survey courses on American history. The presenters said that most students had only very limited exposure to Reconstruction in high school and the survey course may be the only time they get to spend any time on the subject. The professors are from non-elite institutions and they talk about the challenges of reaching students who may not have had great history education before they came to college.
Thanks to Al Mackey at Student of the American Civil War for tipping me off to this video.
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