One of the main similarities between the two events was the killing of innocent people. The Germans and the Puritans motivation was built solely off the fact that they just had something against them. Neither group had a good factual reasoning as to why they treated the people the way they did.
The Salem Witch Trials took place during the 1690s whereas the Holocaust took place during the 1940s. In comparison to the Holocaust having about 20 million deaths the Witch