Blacks had been subject to second-class citizenship by 1900 thanks to the development of Black Codes and Jim Crow Laws. These laws limited the rights guaranteed to black citizens in the US Constitution.
For example, many southern states implemented literacy tests, poll taxes, and the grandfather clause. All three of these obstacles to voting targeted black citizens as their previous status as slaves ensured that they had little/no money, had no formal education, and did not have ancestors who had the ability to vote.
These types of laws were particularly popular in the South due to the fear of blacks taking over the Southern governments. Considering the fact that many blacks were slaves for centuries before 1865, many whites felt that blacks were the inferior race and that they did not deserve the same power/rights as white citizens.