Molecular data has not always been conclusive, but recent phylogenomic analyses indicate that Andalucia is a sister group to the other jakobids, or, in other words, more closely related to them than to the Heterolobosea or Euglenozoa (the other two groups in the Discoba).

[2] The α-tubulin gene of Andalucia more closely resembles that of opisthokonts and diplomonads than its closer relatives, the apparent result of horizontal gene transfer.

[3] As of 2015, the soil heterotroph Andalucia godoyi is the only described species in the genus.

The species Andalucia incarcerata, living in sulfide-rich marine intertidal sediments,[3] was transferred to the genus Stygiella in 2015.

Analysis of DNA sequences from the environment suggests at least two additional species that have not been isolated or formally described.