The Thomas Roland Medal of the Massachusetts Horticultural Society, 1969

The International Plant Propagators' Society Award of Merit, 1973

The Massachusetts Horticultural Society's Jackson Dawson Medal, 1977

The American Association of Nurserymen's Hall of Fame Award, 1983

The Garden Club of America's Medal of Honor, 1983

The Pennsylvania Horticultural Society's Distinguished Achievement Medal, 1983

The Eastern Regional Nurserymen's Association Certificate of Appreciation, 1986

The Scott Horticultural Foundation's Arthur Hoyt Scott Garden Award, 1987

Wayside Gardens' Gold Medal of Honor, 1988

The American Horticultural Society's Catherine H. Sweeney Award, 1992

Flemer is also a director of the National Association of Plant Patent Owners, a Fellow of the Royal Horticultural Society, and a member of the Botanical Society of America and the American Horticultural Society. He was a director of the Chemical Bank of New Jersey and the Landscape Materials Information Service, and presently serves on the White House Grounds Committee, on the Advisory Council for the U.S. National Arboretum, and has served two terms on the Visiting Committee for the Arnold Arboretum.