Two Baton Rouge brothers, who just years ago obtained loans of $30 million from Chase Manhattan Mortgage and Realty Trust, have been indicted by a federal grand jury for, among other things, misapplication of nearly $3 million in funds from rural Louisiana banks, some of which they control.

Roger J. LeBlanc, 29, and his brother, Jules III, 31, both of Baton Rouge, were indicted last Friday on 48 counts. In addition to misapplication of bank funds, they were charged with making false statements to a federal agency and with bank and mail fraud.

Also charged with one count of misapplication was Howard Toler Hatcher, president of Feliciana Bank and Trust Co. in Norwood, La. This is one of several small Louisiana banks controlled by Jules LeBlanc.

The LeBlancs are under investigation by a number of federal agencies for various financial ventures ranging from real estate developments to insurance. The Comptroller of the Currency has probed the LeBlancs' dealings with national banks, the FBI has been looking into the state banking operatios, and the Securities and Exchange Commission has concentrated on Roger's operation of a publicly owned insurance holding company.

The LeBlancs, who are big financial backers of Democratic politicians in Louisiana and elsewher, immediately issued a press release blaming politics for their indictments.

Cheney C. Joseph, interim U.S. attorney in Baton Rouge, would say only that his office stands by the indictment.