1. A gene used to identify a particular bacterial colony or bacteriophage plaque. Such genes are incorporated into cloning vectors to enable the isolation and replication of colonies containing a desired vector. Typically, marker genes confer resistance to specific antibiotics or produce colour changes.

2. (genetic marker) A gene that acts as a tag for another, closely linked, gene. Such markers are used in mapping the order of genes along chromosomes and in following the inheritance of particular genes: genes closely linked to the marker will generally be inherited with it. Markers must be readily identifiable in the phenotype, for instance by controlling an easily observable feature (such as eye colour). See also molecular marker; reporter gene.