The indictment against Catherine Greig, 60, alleges that she conspired with Bulger and others to conceal and harbor the aging gangster during the 16 years the pair were on the run together.
She faces up to five years in prison, three years of supervised release and a $250,000 fine if convicted of the crime.
Greig said she understood the charges against her before softly saying, "Not guilty."
When she entered the courtroom, Greig smiled and nodded to her twin sister and carried on an animated conversation with her lawyer.
Defense attorney Kevin Reddington told reporters after the court appearance that Greig is an excellent candidate for bail and not a flight risk.
"Where's she gonna go? What's the incentive to take off? She's got her family, she's got her sister. She's putting this behind her," he said.
Greig remains behind bars while Reddington prepares additional materials in a request for release. The judge will then decide whether she should be released pending trial.
Reddington would not say whether his client has had any contact with Bulger. There has been no discussion of Greig cooperating with the government or law enforcement, he said.
Greig and the 81-year-old Bulger were arrested on June 22 in their Santa Monica, California, hide-out with a stash of about 30 firearms and $822,000 in cash hidden in holes in the wall.
Greig had used a host of aliases over the years including Carol Gasko, Helen Marshall, Carol Shapeton and Mrs. Thomas Baxter to make purchases and pay bills, according to the indictment.
She ran many of the errands to minimize Bulger's time in public. To erase any suspicion about time spent inside with the window shades drawn, Greig told a property manager at their Santa Monica apartment complex that her husband "Charlie," actually Bulger, was sick with emphysema, the indictment said.
On Wednesday the government released a series of fake identification cards including a New York state ID, Social Security card and AARP membership cards said to have been used by the pair. Some include a photo that resembles Bulger.
Bulger, the former leader of the Winter Hill Gang, was wanted on federal racketeering charges in connection with 19 murders from the 1970s and 1980s. He has pleaded not guilty to all counts against him.
He fled Boston in late 1994 after receiving a tip from a corrupt FBI agent that federal charges were pending. Greig joined him a short time later.
Magistrate Judge Jennifer Boal set a status conference for the Greig case on September 29.
(Editing by Barbara Goldberg and Jerry Norton)
