Jane Buchan is a rarity in the big-money boys’ club of hedge funds.

Amid the testosterone-fueled trading floors of Wall Street, Ms. Buchan has not only built a hugely successful hedge fund investment firm but also one that is, on paper, owned and run by women.

But questions have surfaced about whether her firm, Pacific Alternative Asset Management Company, is now — or ever was — controlled by women at all.

It turns out that S. Donald Sussman, a hedge fund mogul who has bankrolled some of the biggest (male) names in the business, has quietly stood behind Paamco for years, pocketing much of its profit. A recent court ruling officially put a chunk of Paamco’s parent company in his hands.

Equally troubling is the suggestion that Paamco, which collects tens of millions of dollars in fees annually to vet hedge funds for pension funds and other clients, disguised aspects of its own business from its customers, partners and federal regulators.

The arrangement with Mr. Sussman “may have been designed to mislead a number of observers, from the tax authorities to the S.E.C. to entities wishing to invest in women-owned businesses,” Judge Richard J. Sullivan of the United States District Court for the Southern District of New York wrote in an August ruling in the case, which centered on a contract dispute between Mr. Sussman and Paamco.

In an e-mailed statement, Paamco said its relationship with Mr. Sussman had not been structured to mislead anyone and that the transaction in question had been properly treated, and approved by the firm’s legal advisers and auditors.

Furthermore, Paamco said it had never taken any “set aside” business or minority mandates.

A lawyer for Mr. Sussman said in an e-mailed statement that Paamco executives “relied on their own counsel and advisers” and that they had built a “world-class fund of funds business to the benefit of their investors.”

But from the start, Paamco trumpeted the fact that it was run by Ms. Buchan, one of only a handful of women who have made a big mark in the mostly male world of hedge funds.

The question raised by the lawsuit was whether Paamco’s status as a company owned by women, albeit with a scant 51 percent majority for many years, gave it an edge over the competition.

Some states like Illinois and Ohio and corporations like Verizon steer a portion of their pension fund business to investment companies owned by women or minorities, which often fall into the category euphemistically referred to in the industry as “emerging managers.”

For investment professionals trying to stand out in a crowded field, the designation can be “a tool for competitive advantage,” said Thurman V. White Jr., the chief executive officer of Progress Investment Management Company, a San Francisco-based firm that invests in emerging managers. “It’s clear they’ve had some benefits from these kind of initiatives,” he said of Paamco.

Verizon Communications, for instance, hired Paamco as part of the Verizon Diversity Managers program, which was established in the late 1990s to attract funds managed by minorities. Ms. Buchan’s firm oversees a small part of the communication company’s $28.6 billion pension fund. In recent state budget and presentation materials, public pension funds in California and Pennsylvania highlighted Paamco’s status as a firm owned by women.

Documents and depositions related to the case involving Mr. Sussman paint a somewhat different picture. The case centered on whether Mr. Sussman had the right to convert a $2 million loan he made to Paamco’s founding partners in 2000 into an equity stake in Paamco’s parent company. In a countersuit, Paamco’s founding partners claimed the interest Mr. Sussman had charged them violated state laws that set maximum rates on loans.

Paamco, according to the documents, went to great lengths to avoid disclosing that Mr. Sussman had bankrolled its early operations, helped select the name of the firm and had been “periodically” consulted. Moreover, he collected 40 percent of the profit and, at any time, could lay claim to a big stake in the parent company of Paamco.

There was another reason to keep Mr. Sussman off the radar. In 1997, Mr. Sussman, who had earlier withdrawn his investment adviser registration with the Securities and Exchange Commission, settled a claim with the commission that he had failed to disclose a loan he made from a hedge fund he controlled to acquire a building that was used as offices.

In a deposition taken a year ago, James L. Berens, a Paamco co-founder, said there were “two important factors” behind why the firm had structured its relationship with Mr. Sussman as it did: “The first was the potential impact of disclosing Mr. Sussman’s involvement on our Form ADV,” a registration filing with the S.E.C.

“And the second was our — the potential to have status as a majority female-owned entity.”

The designation as women-owned could “lead to consideration for engagement as an investment manager to an extent that otherwise wouldn’t be the case,” Mr. Berens continued. The four founding executives agreed to give Ms. Buchan and another female partner, Judith F. Posnikoff, 51 percent of the firm.

Paamco’s relationship with Mr. Sussman dates back to 2000, when Ms. Buchan and three other individuals approached him about providing financing for a new hedge fund investment venture.

Ms. Buchan, a former All-Ivy League high jumper at Yale who later earned a Ph.D. in business economics from Harvard, was a rising star in the hedge fund world. She had developed a reputation while at another investment firm for digging deep into the records of hedge fund managers to determine what was real and what was fraudulent about their returns.

Mr. Sussman, the founder of Paloma Partners in Greenwich, Conn., provided early financing to dozens of hedge fund managers, including David Shaw of D. E. Shaw & Company.

At first, Mr. Sussman agreed to invest $2 million for a 40 percent ownership stake in the firm with Ms. Buchan and her three partners contributing a total of $10,000, according to the complaint filed last year against Paamco by Mr. Sussman.

But a few weeks later, Ms. Buchan and her partners told Mr. Sussman they wanted his contribution to be made as a loan rather than an equity stake. In doing so, the partners believed they could hide Mr. Sussman’s relationship from investors and regulators, according to the depositions.

Later, when Paamco created the parent company, the principals once again wanted Mr. Sussman off of Paamco’s audited financial statements to keep Paamco’s new partners in the dark about him, Ms. Buchan said in her deposition.

Terms of the loan that Mr. Sussman extended to Paamco were extraordinary. Mr. Sussman was paid the greater of either 10 percent annual interest rate or 40 percent of the company’s profit. From 2003 to 2007, as Paamco’s profit soared, Mr. Sussman collected his share — $55 million, according to his suit.

In addition, after a change in 2002, the loan could be converted into a 40 percent ownership stake in Paamco’s parent at any time. That conversion would have reduced the two women’s share into a minority stake, according to a copy of the loan agreement entered as evidence.

To some, the conversion option raises red flags. “One of the reasons we look at where the money came from to fund the business is if someone has the ability to control something or change something, we are probably not going to certify them or, at least, have different language on the document,” said Janet Harris Lange, president of the National Women Business Owners Corporation. Ms. Lange said Paamco never sought certification from her organization.