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).