LONDON (Fortune) -- Exactly two years ago, I sat in a Moscow courtroom and watched one era in Russian capitalism end. Yukos founder Mikhail Khodorkovsky glumly sat in a cage and awaited the verdict he and everyone else in the courtroom knew was a foregone conclusion: a long Siberian prison sentence, and the dismemberment of Yukos, once Russia's biggest and most-respected firm.

This summer, the new era got firmly underway. In July, Russian energy giant Rosneft went public, with foreign oil firms and investors around the world snapping up shares - other than a few gripes from representatives of now-bankrupt Yukos, few bothered to notice that Rosneft's empire holds what was once Khodorkovsky's crown jewel.

And this past week, Russia's two largest aluminum firms - Rusal and Sual - announced they're considering a merger that would create the largest aluminum company in the world, surpassing familiar North American giants like Alcan (Charts) and Alcoa (Charts).

Unlike Yukos, the new Russian giants are bigger, more dominant, and most important, backed by the Kremlin, even if they're partially owned by oligarchs. In some cases, like in the energy sector, the Russian government holds a controlling stake. In others, the principal oligarchs are careful to always keep Putin in the loop.

It's not what Americans (or even the interventionist French government) would consider traditional capitalism, but it's Putin's preferred model and it's the hallmark of the new Russian capitalism. There's little room for a third way, as Khodorkovsky's case shows.

Like the Rosneft IPO, the merger of the aluminum giants reportedly has Russian President Vladimir Putin's blessing. And unlike Khodorovsky, the owner of Rusal, politically reliable-38-year old Oleg Deripaska, is linked by marriage to Putin's predecessor, Boris Yeltsin, and is famous for his excellent connections in Moscow.

The emergence of Rusal-Sual marks Russia's move beyond just oil and gas to become a global commodities powerhouse. With the incredible rise in demand and price for key commodities like aluminum, steel, iron, nickel and other basic ingredients of industry, Russian companies are likely to be among the key global players.

Earlier in the summer, Russian steel giant Severstal tried and failed to buy a chunk of Arcelor. Although that deal didn't work out, Severstal isn't going anywhere, and it's expected to keep eyeing international assets. Indeed, for the oligarchs that founded Russia's new commodity giants, buying Western companies is effectively a way of getting their cash out of Russia and diversifying their assets, while keeping the Kremlin on board.

Indeed, the Kremlin will still set the rules for any new deals, but Western investors don't seem to mind that. Despite all the grim forecasts that followed the Khodorkovsky trial, the West's appetite for Russian exports is undiminished.

"As long as China's demand for commodities continues, Russia will continue to ride that," says Bill Browder, manager of Hermitage Capital, which has $4 billion under management.

So will Russia's stock market. After pulling back sharply in May amid a global downturn in equities, especially in emerging markets, Russian shares have bounced back, and are now up more than 40 percent so far this year.

"All that petro-capital and commodity demand generates cash that's flowing in every month," says Browder. "There's a whole sector which is booming but hasn't been touched by the stock market, which is real estate. You're also going to see more banks go public like Rosbank, in order to advantage of the demand for Russian shares."

Unless oil goes below $40 a barrel, says Browder, Russian shares should continue to prosper. "Anywhere above $50, Russia is making more money than they know what do with," adds Browder.

What about Khodorkovsky, sitting in a Siberian jail cell, not to mention other political opponents who have been sidelined - or worse - by the Kremlin? "As an investor, you have to leave your emotions and sentimentality at the door," says Browder. He should know - the Russian government has refused him entry since blocking his visa last November, despite his status as Russia's leading foreign money manager. Apparently Browder's push for greater shareholder rights offended the wrong people in Kremlin, leaving him out in the cold.

Like many Russian exiles before him - or the investors who lost billions in Yukos but haven't stayed away - Russia's brutal politics haven't dimmed Browder's ardor for a country he can only watch from London. "I'm a believer," he says, "despite my short-term travel problems."