In June of 1982, a symposium entitled “Evolution of Genes and Proteins“ was held at the State University of New York at Stony Brook in conjunction with the joint meeting of the Society for the Study of Evolution and the American Society of Naturalists. At that symposium, Masatoshi Nei invited a group of molecular evolutionists for a meeting to start a new journal called Molecular Biology and Evolution. This proposal was approved by the majority of the attendants, and the journal was started in December 1983, with Walter Fitch as Editor-in-Chief and Masatoshi Nei as Managing Editor. The purpose of this journal was (1) to generate better communication between molecular biologists and evolutionary biologists, (2) to rapidly publish high-quality papers, (3) to make the journal available to a large international readership at an affordable price, and (4) to put forward a journal that is owned and controlled by the scientific community. To ensure the latter point, the Society for Molecular Biology and Evolution was formed. The Society has since held sole ownership of Molecular Biology and Evolution. Initially, the Society consisted of the Editor-in-Chief, the Managing Editor, the Associate Editors, and the Editorial Board Members.

The University of Chicago Press agreed to publish Molecular Biology and Evolution, and Volume 1 of the journal consisting of 6 issues was published in 1983-1984. By 1985 Molecular Biology and Evolution was ranked third among evolutionary journals on the basis of its Impact Factor, exceeded only by Genetics and Evolution. By 1991 it had become the leading journal in Evolutionary Biology.

In 1992, an International Symposium on Molecular Evolution at Pennsylvania State University was organized. At that meeting Masatoshi Nei and Walter Fitch proposed that the Society for Molecular Biology and Evolution become an active society with all individual subscribers becoming members. That proposal was enthusiastically endorsed by those present at the meeting. Walter Fitch was elected as the first President of the Society, Masatoshi Nei was chosen as President-Elect, Linda Maxson was elected as Secretary-Treasurer, Caro-Beth Stewart was elected as interim Councilor, and Barry Hall was elected as Editor of Molecular Biology and Evolution starting with Volume 11 in 1994. These five individuals were charged with the organization of a functional society and the writing of its bylaws. The Society officially activated on January 1, 1993.

The Society for Molecular Biology and Evolution is governed by a Council, which originally consisted of the President, Past-President, President-Elect, Secretary-Treasurer, and Editor-in-Chief of Molecular Biology and Evolution. Effective January 1994, the office of Treasurer was added to the Council, with Richard Hudson being elected as the first Treasurer. Effective January 1996, the Council was expanded to include three Councilors, each serving overlapping three-year terms. In 2008, the bylaws were amended, and the council currently consists of the immediate Past-President, President, President-Elect, Secretary, Treasurer, and three elected Councilors. In 2011, the number of Councilors was increased to six.

In 1994, the Council decided to assume publication of Molecular Biology and Evolution, thus ending its association with University of Chicago Press with the completion of Volume 12 in 1995. This decision gave the Society full financial control of the journal, and Allen Press was chosen to publish Molecular Biology and Evolution on behalf of the Society. By the end of 1995 Molecular Biology and Evolution had increased more than threefold in size, and the number of issues per volume was increased to ten. Molecular Biology and Evolution became a monthly journal in 1997 (Volume 14). In 2003, Oxford University Press became the publisher of Molecular Biology and Evolution on behalf of the Society. Since 2005, MBE has been publishing 250-300 papers per year and remained at the forefront of its field.

In 2008, the Council voted to create a second Society journal, Genome Biology and Evolution, with Takashi Gojobori as Founding Editor and William Martin as Editor-in-Chief. The Society owns Genome Biology and Evolution and contracted with Oxford University Press for publication. The motivation for establishing the new journal came from the growth of genomics and, as a consequence, the growth of genome-oriented evolutionary research. The first volume of GBE appeared in 2009.

The annual meetings of SMBE have grown in scope and significance. They regularly draw over 800 participants and have witnessed a dramatic increase in SMBE-sponsored awards and prizes for young scientists.