Transgenes are genes that have moved or been transferred between two different organisms, or lines by means other than sexual reproduction. Natural causes of such transfers, sometimes called lateral or horizontal gene transfer, include being carried by viruses or bacteria that are able to transfer DNA between different species. There are numerous, diverse mechanisms that allow a low frequency of gene movement between species, such as accidental fusion of cells between different species, or the injection of DNA by bacteria into plant cells. Cumulatively, and over time, these mechanisms lead to widespread gene flow between very different types of organisms, and recent advances in genomics show that transgenes are common and widespread in most, if not all lineages.

In common use the term transgene refers to genes that have been deliberately introduced into a particular organism by laboratory manipulation. Transgenes are recognizable by their DNA sequence, or by their anomalous pattern of divergence in DNA sequence among the family tree pattern of DNA similarity shown by related species. Mobile parasitic DNAs ( e.g.transposons, and MULE parasites found in rice and millet) are a commonest example of transgenic genes found in food crops.