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Charles Cantor (born 1942) is an American molecular geneticist who, in conjunction with David Schwartz, developed pulse field gel electrophoresis for very large DNA molecules. His 3 vol book, biophysical chemistry, co-authored with Paul Schimmel, was an influential textbook in the 1980s and 1990s.

Charles Cantor is Director of the Center for Advanced Biotechnology at Boston University. He is currently on a two-year sabbatical acting as Chief Scientific Officer at Sequenom, Inc. However, his research laboratory at Boston University continues to be active, and he works there frequently. He is also a co-founder and Director of Retrotope, a US-based company using heavier isotopes of carbon (C13) and hydrogen (deuterium) to stabilize essential compounds like amino acids, nucleic acids and lipids to target age-related diseases.