Charles L. (Lindy) Marinaccio, one of the two Democratic members of the Securities and Exchange Commission, announced yesterday that he will not seek reappointment when his term expires June 5.

In a letter to Chairman John S.R. Shad, Marinaccio said he wanted to return to the private sector after his 24 years of federal service, including stints with the Justice Department, the Federal Reserve Board, and the Senate Banking, Housing and Urban Affairs Committee. He will have served just over a year at the SEC.

His departure will leave the five-member SEC with a bare quorum of three. Republican James C. Treadway Jr. announced in January that he would leave this spring, two years before the end of his term QUESTIONS ABOUT EDGAR . . .

The House Energy and Commerce subcommittee on oversight and investigations plans to hold a hearing Thursday on EDGAR, the acronym for the SEC's new electronic data analysis and retrieval system. The computerized system allows corporations to transmit their SEC reports electronically over telephone lines or by sending the SEC a magnetic tape. The staff contends that EDGAR is behind schedule and 50 percent over budget. Investigators allege that it does not meet technical specifications and cannot analyze filings.

The SEC receives about six million pieces of paper annually. Electronic filing, which is supposed to save billions of dollars, has been a priority item under Shad. The program is expected to cost $5.1 million this fiscal year; the agency has requested an additional $3.3 million for next year.

Six months after the pilot program began, 144 companies have filed 450 pieces of information. The second phase of the program began last month when the state securities commissions of California, Georgia and Wisconsin began to receive the same data electronically.

Under the next phase, files will be indexed and computerized searches will be possible. Investors using personal computers will be able to have access to the data, beginning next March. Plans calls for the system to become fully operational -- receiving filings from the 10,000 public companies -- by the end of 1988. MERGING THE REGULATORS . . .

At a recent convention of the futures industry, Rep. Edward R. Madigan (Ill.), the ranking Republican on the House Agriculture Committee, which has jurisdiction over the Commodity Futures Trading Commission, contended that the large staff of the House Energy and Commerce Committee eventually will try to take over oversight of the CFTC. Its subcommittee on telecommunications already has jurisdiction over securities and the SEC.

"I have no doubt that committee chairman John Dingell D-Mich. wants jurisdiction over the moon and the stars," Madigan said. GOOD-BYE CERTIFICATES? . . .

If the SEC had its way, companies would abolish printed stock certificates. Shad told industry representatives that hundreds of millions of dollars annually could be saved by switching to a system in which brokers would supply clients with computerized records of their stock transactions.

Existing certificates gradually would be "immobilized" in central depositories and ownership of the securities would be transferred electronically. About half of corporate stock certificates are now immobilized.

-- Nancy L. Ross