Meselson, who was born in Denver, Colorado, studied liberal arts at the University of Chicago and physical chemistry at the California Institute of Technology, Pasadena. After he obtained his PhD in 1957 he remained at the Institute until 1960 when he moved to Harvard, where he served from 1964 as professor of biology and from 1976 as Thomas Dudley Cabot professor of natural sciences.

In 1957 Meselson, in collaboration with the American biologist Franklin Stahl (1910– ), conducted one of the classic experiments of molecular biology, which clearly revealed the semiconservative nature of DNA replication. It seemed likely that when the double helix of DNA duplicated, each new helix, and hence each daughter cell, would contain one DNA strand from the original helix; in the jargon of the time, replication would be semiconservative. The other possibility was that one daughter molecule would contain both the old strands and the other daughter molecule both the new strands – conservative replication.

Meselson and Stahl grew many generations of the bacterium Escherichia coli on a simple culture medium containing ammonium chloride (NH₄Cl), labeled with the heavy isotope of nitrogen, ¹⁵N, as the only nitrogen source. They then added normal ¹⁴N nitrogen to the medium and removed bacterial cells at intervals, extracting their DNA by ultracentrifugation. The density of the DNA in successive samples could be determined by the method of equilibrium density gradient centrifugation, in which samples of differing density diffuse into discrete bands corresponding to their own effective density. Ultraviolet absorption photographs of these bands allowed the concentration of DNA in each band to be determined. The results showed that (following the introduction of ¹⁴N) after one doubling of the E. coli bacteria all the DNA molecules contained equal amounts of ¹⁵N and ¹⁴N, i.e., they were all half labeled. After two generations there were equal amounts of half-labeled DNA molecules and wholly ¹⁴N molecules. This effectively demonstrated that replication is semiconservative. The results were published in the Proceedings of the National Academy of Sciences, as The Replication of DNA in Escherichia coli (1958).

Meselson has also worked with Sidney Brenner and François Jacob on the mechanism of viral infection. In 1961, working with the virus T4, they showed that on invasion of a host bacterial cell the viral DNA releases messenger RNA, which, when it arrives at the host ribosomes, instructs these to make viral protein rather than bacterial proteins.