As well as including gene reports for genes derived from species within the family Drosophilidae, FlyBase also includes gene reports for non-drosophilid genes ("foreign genes") that have been introduced into Drosophila, for example via transgenic constructs. Summary information as to the origin of these "foreign genes" is curated by FlyBase and attributed to this publication.

For each foreign gene, curators create a formatted line attributed to this publication, consisting of the species that the gene is derived from, its symbol, and where possible an accession number for the gene (either an identifier number from a model organism database, or a sequence accession number).

FlyBase also includes gene reports for engineered "tags", which are defined as a DNA fragment, artificial or from an endogenous or foreign gene, that is used to mark a gene product, either its transcript or protein. This includes epitope tags such as "Avic\GFP" and function tags such as nuclear localization signals. Summary information as to the origin of these "tags" is curated by FlyBase and attributed to this publication.

For each tag, curators create a formatted line attributed to this publication, consisting of the species that the DNA fragment is derived from, the type of tag (e.g. epitope tag), its symbol, and where possible an accession number for the DNA fragment (either an identifier number from a model organism database, or a sequence accession number) or a brief description of the nature of the tag.