In the morass of litigation generated by the subprime crisis, few suits have targeted law firms over their roles advising companies that fueled the mortgage bubble.

But a big exception–an investor class action against Greenberg Traurig and Quarles & Brady–is barreling along in Phoenix, Ariz., federal district court. On Tuesday Judge Frederick Martone certified two classes of investors in the case, which targets the two firms over their roles in an alleged Ponzi scheme run by real estate lender Mortgages Ltd. The investors claim they suffered $900 million in losses as a result of the alleged fraud.

Both law firms expressed disappointment with the ruling. “We empathize with the investors who lost money but their investments were in loans that, unfortunately, fell victim to the collapse of the real estate market,” Greenberg Traurig said in a statement. “[W]e continue to believe that when the facts are fully presented, they will show that our firm and its lawyers acted appropriately and that the claim against them is without merit.”

Quarles counsel Robert Gooding of Morgan Lewis & Bockius said in a statement that “the firm is disappointed by the recent class certification decision, but will continue to vigorously defend the action.” Quarles & Brady, which had advised a company called Radical Bunny that helped find investors for Mortgage Ltd., has previously said its conduct was “at all times lawful and ethical.”

Andrew Friedman of Bonnett, Fairbourn, Friedman & Balint, co-lead counsel for the plaintiffs, told us the decision was “very unusual” given the challenges of bringing investor claims against professional advisors like lawyers and accountants. “The class cert opinion is an important step forward for investors who lost so much,” Friedman said.

In its 2008 ruling in Stoneridge v. Scientific-Atlanta, the U.S. Supreme Court severely curtailed the scope of federal securities claims for aiding and abetting by third-party advisors. But the case against Greenberg Traurig and Quarles & Brady was brought under Arizona’s so-called blue-sky laws, which Friedman said “are very protective of investors and remedial in nature.”

As it stands, both firms face claims for primary liability and aiding and abetting the alleged fraud by Mortages Ltd. and Radical Bunny. In a separate order on Monday, Judge Martone pared down some of the claims against Greenberg Traurig, which is represented by Williams & Connolly.

In the years before it collapsed, Mortgages Ltd. made high-interest loans to real estate developers that it then sold off to investors. The plaintiffs allege that the company was insolvent by 2005 but continued–with the help of Radical Bunny–to raise money to pay past investors and to fund the “extravagant” lifestyle of CEO Scott Coles.

Then the real estate market collapsed, making it impossible for Mortgages Ltd. to continue making loans. Coles committed suicide in June 2008, and his company filed for bankruptcy two weeks later. Radical Bunny followed with a bankruptcy filing in October 2008. The Securities and Exchange Commission has since claimed that Mortgages Ltd. willfully violated securities laws and charged the founders of Radical Bunny with making false and misleading statements to investors.

In their complaint, lawyers for the investors at Bonnett Fairbourn and Tiffany & Bosco claim the companies “could not have perpetrated and concealed a fraud so massive without the complicity of lawyers and accountants,” including Greenberg Traurig and Quarles & Brady. Beginning in 2006, Greenberg Traurig advised Mortgages Ltd. on 11 private-offering memorandums for investors, and the complaint claims that lead partner Robert Kant was “fully aware” that the company was being funded through Radical Bunny’s illegal securities sales.

Quarles & Brady, which advised Radical Bunny, also knew its client was breaking the law, the complaint alleges. The partner in charge of advising the company on securities issues, Chris Hoffmann, later told the SEC that he had serious concerns about the sales and whether the business had a “a Ponzi scheme feel,” according the plaintiffs.

The lawsuit, filed in 2010, initially also targeted Mortgages Ltd. and Radical Bunny. The bankrupt companies were later voluntarily dismissed. The judge also dismissed claims against their accountants.

The class action is the just one of several suits pending against the firms related to Mortgages Ltd., though it has progressed the furthest. In March 2011, the liquidation trustee for Mortgages Ltd. sued Greenberg Traurig for malpractice in Arizona state court. The firm was also hit with a separate investor class action in California state court in February.