John Clark Middleton, 99, a retired accountant with the old Capital Transit Co. and an organist at several churches in the Washington area, died of pneumonia Dec. 30 at the Martha Jefferson Hospital in Charlottesville, Va.

Mr. Middleton was born in Washington. His family occupied the Woodley property, which is now the Maret School on Cathedral Avenue NW, and later "Lone Oak," a nearby property which now belongs to the Swiss Embassy.

At the age of 16, Mr. Middleton succeeded his mother as organist and choir director at St. Alban's Episcopal Church, of which he was a life member. He held that post for about 15 years and later played at other churches here.

He worked for the American Security and Trust Co. and the U.S. Shipping Board before joining Capital Transit as an accountant. He retired about 1950 and moved to Orange, Va., in 1970.

During World War II, at the age of 59, he received a commission as a lieutenant in the Coast Guard and commanded a number of small vessels in the Chesapeake Bay and the Atlantic.

He was a Mason and a member of the Corinthian Yacht Club.

His wife, Margaret Coyne Middleton, died in 1979.

Survivors include two daughters, Mrs. Van T. Smith of Orange, and Mrs. Frank Bromwich of Ridgeway, Ontario, Canada; six grandchildren, and 12 great-grandchildren.