The type for the genus is Amphidinium operculatum Claparède & Lachmann.

The genus includes the species Amphidinium carterae which is used as a model organism.

[2][3] There are reports of minicircles that do not have known transcripts, like in the Amphidinium carterae chloroplast genome,[3] although these were not found in the Symbiodinium sp.

[2] Minicircle-derived transcripts can be processed in ways not typical of eukaryotes, including the addition of a 3' poly(U) tail,[3] as opposed to the typical poly(A) tail derived from polyadenylation of eukaryotic transcripts.

Minicircle-derived antisense transcripts are also produced, but without 3' poly(U) tails.