Amid bearish comments on banks, the American Banker index of 225 banking stocks fell 0.37% Thursday.
In the broader market, the Standard & Poor's 500 rose 0.47%.
The big gainers included Santander Bancorp of San Juan, Puerto Rico, which rose 4.7% after rising 4.6% Wednesday and 4.3% Tuesday.
Investors may have been buying Santander's stock on the lows. Its shares have fallen in the past two months along with those of Puerto Rican banking companies that have disclosed financial and accounting problems, though Santander has not reported such problems. Last week Santander's stock hit a 52-week low.
Decliners included three California banking companies: Cathay General Bancorp of Los Angeles, down 2.3%, UCBH Holdings Inc. of San Francisco, 2.8%, and EastWest Bancorp Inc. of San Marino, 1.4%. Sandler O'Neill & Partners LP analyst Brian Conn lowered his rating on all three to "hold" from "buy" because of recent runups in their stock.
Two analysts expressed concern about banking in reports issued Thursday.
With net interest margins expected to remain under pressure from rising deposit costs, Morgan Stanley prefers U.S. large-cap banks to mid-caps, Christopher Chouinard wrote.
"The mid-caps are trading at a valuation premium to the large-caps, and rely more on net interest income for revenue and profits," he wrote. "For the large-caps, we think high dividends and share buybacks offset decelerating earnings growth."
Lee Calfo, the head of bank research at Cohen Brothers & Co., wrote that "bank and thrift fundamentals have taken a turn for the worse" because of pressure on net interest margins, credit quality concerns, and historically high valuations.
Mr. Calfo lowered his outlook on the commercial banking to "cautious" from "neutral" and maintained his "cautious" outlook on the thrift field."
Big gainers besides Santander included Commercial Capital Bancorp. Inc. of Irvine, Calif., up 3.9%, and Great Southern Bancorp Inc. of Springfield, Mo., up 3.5%.
Bancorp Rhode Island Inc. of Providence fell 3.6%, 1st Source Corp. of South Bend, Ind., fell 3.5%, and First Financial Corp. of Terre Haute, Ind., fell 3.5%.
