He led a productive genetics research lab both at Purdue University and as the James G. Boswell Professor of Neuroscience, emeritus, at the California Institute of Technology.

[2][3][9] At Brooklyn College, as a sixteen-year-old freshman, Benzer met Dorothy Vlosky (nicknamed Dotty), a twenty-one-year-old nurse.

This catalyzed Benzer's shift in interest to biology, and he moved into the area of bacteriophage genetics.,[10] spending two years as a postdoctoral fellow in Max Delbrück's laboratory at California Institute of Technology, and then returning to Purdue.

Benzer realized that by generating many r mutants and recording the recombination frequency between different r strains, one could create a detailed map of the gene, much as Alfred Sturtevant had done for chromosomes.

In his molecular biology period, Benzer dissected the fine structure of a single gene, laying down the ground work for decades of mutation analysis and genetic engineering, and setting up a paradigm using the rII phage that would later be used by Francis Crick and Sydney Brenner to establish the triplet code of DNA.

This translated to methodological differences in the two researchers' experiments with Drosophila that profoundly influenced the field of behavioral genetics.

[10] To better identify mutants, Benzer developed novel apparatuses such as the countercurrent device, which was designed to separate flies according to the magnitude and direction of their phototactic response.

[15] Benzer identified mutants for a wide variety of characteristics: vision (nonphototactic, negative phototactic, and eyes absent[16]), locomotion (sluggish, uncoordinated), stress sensitivity (freaked-out), sexual function (savoir-faire, fruitless), nerve and muscle function (photoreceptor degeneration, drop-dead), and learning and memory (rutabaga, dunce[17]).

[19] To monitor Drosophila locomotor activity, Benzer and postdoctoral researcher, Yoshiki Hotta, designed a system using infrared light and solar cells.

[19] All three mutations were mapped to the X chromosome, zero centimorgans away from each other, indicating that the mutant phenotypes corresponded to alleles of the same gene, which Konopka named period.

He also contributed to the field of aging biology, looking for mutants with altered longevity and trying to dissect the mechanisms by which an organism can escape the inevitable functional downfall and its associated diseases.

[21] In 1998, Benzer and his colleagues Yi-Jyun Lin and Laurent Seroude published findings of a long-life mutant in Drosophila, then named Methuselah.