The hottest trade of the past two months has been a surprising one: Going long the U.S. dollar against other currencies. And the recent dollar strength appears to have had a profoundly negative impact on commodity prices.

Since the end of June, the U.S. Dollar Index (which compares the dollar to a basket of other currencies) has risen 3.5 percent, bringing the index to a 52-week high. And while the weakness in the widely watched euro has certainly contributed to the move, the dollar has also shown considerable strength against currencies like the British pound, the Canadian dollar and the Japanese yen. On Tuesday alone, the dollar rose 0.7 percent against the yen—a serious move for a major currency.

Many expect the European Central Bank to announce easing measures this week, and this expectation is likely contributing to euro weakness and thus dollar strength. But because the move is so broad-based, it can't all be credited to ECB President Mario Draghi.

Read More The wait is over for dollar bulls

"This is much more about the widening gap between the U.S. economy and economic performance in the rest of the world," said Kathy Lien, managing director of FX Strategy at BK Asset Management. "In the U.S., we're seeing a widening divergence between economic growth and monetary policy outlook," which should ultimately lead interest rates to rise. "And as we get more discouraging news from Japan, from the euro zone, etc., that will also boost the attractiveness of the U.S. dollar."

The dollar rally certainly hasn't been celebrated by commodity bulls, who saw gold hit a 2½-month low on Tuesday, and crude plunge by more than 3 percent. Broadly speaking, commodities tend to move inversely to the dollar. This makes sense, given that as each dollar becomes worth more, it should take fewer of them to buy the same amount of hard assets. Most commodities are priced in U.S. dollars.

"Right now, the dollar is the dog, and every other market is just the tail," Jim Iuorio, managing director at TJM Institutional Services, said Tuesday on CNBC's "Futures Now." "I think the backbeat of all these commodity moves is the dollar."

Read More Commodities are flashing a warning sign

In fact, over the past 30 days, crude oil and the dollar have enjoyed a correlation of negative 0.88—meaning they moved in almost completely opposite directions—according to Stephen Schork, the editor of the widely read Schork Report. (Exact opposites would score a negative 1.0.)

Schork, however, doesn't think the move can all be pegged to the dollar, explaining that it's "more of a coincidence." He says the key catalyst in the energy space has been the end of driving season, which reduces the discretionary need for gasoline.

Still, with potential for the dollar's run to continue this week due to Thursday's ECB decision and Friday's U.S. employment report, Lien would advise against buying into beaten-down commodities just yet.

"I think you're going to see further decline in commodities, along the lines of 4 to 5 percent," Lien told CNBC.com. "So I would wait for them to become a bargain."

—By CNBC's Alex Rosenberg

Watch "Futures Now" Tuesdays and Thursdays at 1 p.m. ET exclusively on FuturesNow.CNBC.com!