Compensation for female CEOs fell 18.5 percent, compared with 6.1 percent for men, according to The Corporate Library. Both men and women were hit hard by falling share prices, which shrank the value of stock options and grants that often make up a huge portion of CEO pay.

All told, female chief executives made just 58 percent as much as their male counterparts, the Corporate Library found.

Among the factors causing the disparity: Women are less likely to lead huge companies and they're more commonly found at the helm of companies in hard-hit industries like retail, said Corporate Library researcher Greg Ruel in an interview.

"They tend to be concentrated at smaller companies, whereas at larger companies, they're just not there yet," Ruel said.

Notably, there are no female CEOs at the biggest Wall Street firms. Last year, Citigroup (C) paid 21 of its managers a total of $390 million and Bank of America (BAC) paid $227 million to 13 executives. The average of all that compensation is about $18 million per person. And strong results this year by Goldman Sachs (GS) and others will likely spur record compensation, many believe. These companies' CEOs will be paid handsomely, too, but all of them are men. (Whether more women atop Wall Street's leading banks would have helped to avert the financial crisis is another question.)

But there's another big issue that complicates any look at executive pay and gender. Ruel looked at compensation for CEOs of some 3,300 companies -- basically members of the Russell 3000 index and a relative handful of those just outside it -- and only 78 of them were women.

According to Ruel, Meg Whitman (EBAY) was the highest-paid female CEO of 2007. But she stepped down late that year and no other woman came close in 2008 to making what she did. In fact, of last year's 150 top paid chief executives, only one, Martine A. Rothblatt of United Therapeutics Corp. (UTHR), was a woman.