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In OoTP right after Sirius Black's death when Voldemort shows up Bellatrix says something along the lines of "I killed the animagus Black" Not sure if that is the exact quote or not.
But supposedly not many people knew about Sirius being an animagus. So how did Bellatrix Lestrange find out?
The Death Eaters knew Sirius was an Animagus, as was confirmed by Draco Malfoy when Sirius came to King's Cross station drop Harry off in Harry Potter and the Order of the Phoenix.
“I seem to have touched a nerve,” said Malfoy, smirking. “Well, just watch yourself, Potter, because I’ll be dogging your footsteps in case you step out of line.”
“Get out!” said Hermione, standing up. Sniggering, Malfoy gave Harry a last malicious look and departed, Crabbe and Goyle lumbering in his wake. Hermione slammed the compartment door behind them and turned to look at Harry, who knew at once that she, like him, had registered what Malfoy had said and been just as unnerved by it...
...He exchanged another nervous look with Hermione and then stared out of the window. He had thought Sirius coming with him to the station was a bit of a laugh, but suddenly it seemed reckless, if not downright dangerous. . . . Hermione had been right. . . . Sirius should not have come. What if Mr. Malfoy had noticed the black dog and told Draco, ...
Harry's thoughts imply Lucius Malfoy could have recognized Sirius' animagus disgiuse himself, thus implying that most of the death eaters would know of it anyway.
She was (still) in Azkaban when Sirius escaped, and might have noticed how he did that.
Alternately, Pettigrew told her during the time they were both major Death Eaters (i.e. sometime during Harry's fifth year). That might actually be more likely.
