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A gap gene is a type of gene involved in the development of segmented embryos. Gap genes are defined by the effect of a mutation in that gene, which causes the loss of contiguous body segments, resembling a gap in the normal body plan. Each gap gene, therefore, is necessary for the development of a section of the organism.

Gap genes were first described by Christiane Nusslein-Volhard and Eric Wieschaus in 1980. They used a genetic screen to identify genes required for embryonic development in the fruit fly Drosophila melanogaster. They found three genes – knirps, Krüppel and hunchback – where mutations caused deletion of particular stretches of segments.

encodes transcription factors in a developing embryo. They fall under the class of segmentation genes that are expressed during embryonic morphogenesis. Mutations in gap genes are responsible for the loss of contiguous body segments. Evolutionary biologists and molecular cell biologists, study morphogenesis by observing the effects of mutations in the process of development. From experiments that studied these effects in the common fruit-fly (Drosophila melanogaster), four gap genes have been characterised; Kruppel, giant, hunchback tailless & knirps. Each of these genes are expressed in characteristic regions of the developing embryo under the control of maternal effect genes such as bicoid and nanos.