Federal authorities announced Thursday a raft of criminal charges against SAC Capital, the hedge fund run by the billionaire Steven A. Cohen, an unusually aggressive move that could cripple one of Wall Street's most successful stock trading firms.

In the 41-page indictment that includes four counts of securities fraud and one count of wire fraud, prosecutors charged the fund and its units with carrying out a broad insider trading scheme between 1999 and 2010. The case seeks to attribute certain criminal acts of employees to the company itself.

The indictment also takes aim at SAC for "an institutional indifference" to wrongdoing that "resulted in insider trading that was substantial, pervasive and on a scale without known precedent in the hedge fund industry."

The case, announced by federal prosecutors and the FBI in Manhattan, is the culmination of an investigation that spanned a decade. As the federal government mounted a relentless crackdown against insider trading, an investigation that reached into corporate board rooms and Wall Street trading floors, it zeroed in on Cohen as a central target.

Without evidence directly linking Cohen to illicit trades, the government stopped short of criminally charging him. But the case is a blow to him all the same. Not only does the firm name bear his initials, but Cohen also owns 100 percent of the firm he founded with his own money more than two decades ago.

Cohen, 57, an avid collector of art and real estate, also faces civil charges. The indictment Thursday comes on the heels of the Securities and Exchange Commission's filing a civil action last week that accused Cohen of failing to supervise employees suspected of insider trading.

The government's effort to root out insider trading on Wall Street has swept up more than 80 people; of those, 73 have either been convicted or pleaded guilty.

But Thursday's indictment against SAC represents a new phase in the investigation. Criminal charges against large companies are rare, given the collateral consequences for the economy and innocent employees. After the Justice Department indicted Enron's accounting firm, Arthur Andersen, in 2002, the firm collapsed and 28,000 jobs were lost.

In the SAC case, the indictment could deliver a death blow to the fund. Already, amid several guilty pleas by former SAC employees and a series of civil actions brought by federal securities regulators, the fund's investors have pulled about $5 billion of $6 billion in outside money from the firm. Those that have withdrawn money include major financial-industry players like Blackstone Group and Citigroup.

That exodus could gain steam in the wake of the indictment. SAC also must assuage concerns from Goldman Sachs and other large banks that trade with SAC and finance its operations. There is little precedent for what a criminal charge would mean for SAC and its banking relationships, but legal experts said that an indictment could trigger default provisions in the fund's agreements with its trading partners, meaning that it would force brokerage firms to stop doing business with the fund.

But the charges won't necessarily destroy SAC. Until now, Cohen has been largely shielded from the crippling effects of mass investor withdrawals. Of the $15 billion that SAC managed at the beginning of the year, about $8 billion is Cohen's.

One option for Cohen would be to shut down SAC and open up a so-called "family office" that managed his own fortune. But Securities and Exchange Commission, as part of a civil action filed against Cohen last week that accuses him of failing to supervise his employees, could seek to have him banned from the financial-services industry for life, an outcome that would prohibit him from trading stocks.

Cohen could also deploy his deep Wall Street Rolodex to sustain the fund. He sits on the vaunted board of the Robin Hood Foundation, a nonprofit fighting poverty, with David M. Solomon, the co-head of investment banking at Goldman Sachs. He also serves as a trustee of Brown University, alongside Brian T. Moynihan, the chief executive of Bank of America. (One of Cohen's seven children graduated from Brown.)