Some people think it was the bubonic plague because that matches _some_ of the symptoms reported at the time and y. pestis has been found in mass graves from the period. (Obviously people who disagree are pulling out the "correlation does not equal causation" card.)
Other people believe it was ebola, anthrax, or something else because the incubation period, the rate and nature of the spread, and some of the symptoms don't match those of the modern bubonic plague.
Some people believe it was the y. pestis, but it behaved differently back then because humans had zero immunity when it was introduced, and both humans and the bacteria have had a few centuries to evolve since then.
And some people believe that it wasn't just one disease that was responsible for the black death but a number of different diseases sweeping through around the same time. They didn't know much about disease at the time, and if everyone has heard of the black death and a bunch of people get sick and die, everyone is going to blame it on the black death.
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