The subfamily is monophyletic (Grimaldi 1990; Sidorenko 2002), but can not be characterised by a single morphological character that distinguishes this subfamily from the Drosophilinae. See for a discussion on this subfamily "Drosophila: A Laboratory Handbook" by M. Ashburner, S. Hawley, K. Golic (not reproduced here due to copyrights).

• D. A. Grimaldi 1990. A phylogenetic, revised classification of genera in the Drosophilidae (Diptera). Bulletin of the American Museum of Natural History 197: 1–128.
• V. S. Sidorenko 2002. Phylogeny of the tribe Steganini Hendel and some related taxa (Diptera, Drosophilidae). Far Eastern Entomologist 111: 1-20.

The phylogenetic relationships within the subfamily have not yet been confirmed by molecular studies, and are partially based on traditional cladistic methods using primarily morphological characteristics and partly based on expert opinions. The classification below might be not approved by all scholars in the field, but gives a reasonable overview of our current knowledge:

Tribe: Steganini

Subtribe: Steganina

Genus: Eostegana

Genus: Stegana

Subtribe: Leucophengina

Genus: Allopygaea

Genus: Cacoxenus ^[1]

Genus: Leucophenga

Tribe: Gitonini

Subtribe: Gitonina

Genus: Amiota

Genus: Apenthecia

Genus: Apsiphortica

Genus: Cacoxenus

Genus: Crincosia

Genus: Erima

Genus: Gitona

Genus: Paraleucophenga

Genus: Paraphortica

Genus: Phortica

Subtribe: Acletoxenina

Genus: Acletoxenus

Genus: Hyalistata

Genus: Mayagueza

Genus: Pseudiastata

Genus: Rhinoleucophenga

Genus: Trachyleucophenga

Subtribe unknown

Genus: Electrophortica

Genus: Pararhinoleucophenga

Genus: Parastegana

Genus: Pseudostegana

Tribe unknown

Genus: Soederbomia

Genus: Pyrgometopa

For species within the various genera, see fix Taxodros