A cistron is a region of DNA that is conceptually equivalent to some definitions of a gene, such that the terms are synonymous from certain viewpoints,^[1] especially with regard to the molecular gene as contrasted with the Mendelian gene. The question of which scope of a subset of DNA (that is, how large a segment of DNA) constitutes a unit of selection is the question that governs whether cistrons are the same thing as genes. The word cistron is used to emphasize that molecular genes exhibit a specific behavior in a complementation test (cis-trans test); distinct positions (or loci) within a genome are cistronic.

The words cistron and gene were coined before the advancing state of biology made it clear to many people that the concepts they refer to, at least in some senses of the word gene, are either equivalent or nearly so. The same historical naming practices are responsible for many of the synonyms in the life sciences.

The term cistron was coined by Seymour Benzer in an article entitled The elementary units of heredity.^[2] The cistron was defined by an operational test applicable to most organisms that is sometimes referred to as a cis-trans test, but more often as a complementation test.

Richard Dawkins in his influential book The Selfish Gene argues against the cistron being the unit of selection and against it being the best definition of a gene. (He also argues against group selection.) He does not argue against the existence of cistrons, or their being elementary, but rather against the idea that natural selection selects them; he argues that it used to, back in earlier eras of life's development, but not anymore. He defines a gene as a larger unit, which others may now call gene clusters, as the unit of selection. He also defines replicators, more general than cistrons and genes, in this gene-centered view of evolution.

Defining a Cistron as a segment of DNA coding for a polypeptide, the structural gene in a transcription unit could be said as monocistronic (mostly in eukaryotes) or polycistronic (mostly in bacteria and prokaryotes). For example, suppose a mutation at a chromosome position is responsible for a change in recessive trait in a diploid organism (where chromosomes come in pairs). We say that the mutation is recessive because the organism will exhibit the wild type phenotype (ordinary trait) unless both chromosomes of a pair have the mutation (homozygous mutation). Similarly, suppose a mutation at another position, , is responsible for the same recessive trait. The positions and are said to be within the same cistron when an organism that has the mutation at on one chromosome and has the mutation at position on the paired chromosome exhibits the recessive trait even though the organism is not homozygous for either mutation. When instead the wild type trait is expressed, the positions are said to belong to distinct cistrons / genes. Or simply put, mutations on the same cistrons will not complement; as opposed to mutations on different cistrons may complement (see Benzer's T4 bacteriophage experiments T4 rII system).

For example, an operon is a stretch of DNA that is transcribed to create a contiguous segment of RNA, but contains more than one cistron / gene. The operon is said to be polycistronic, whereas ordinary genes are said to be monocistronic.