Due to its morphological similarity to the genus Multiclavula, its isolated phylogenetic position (distinct from all other orders based on molecular data) was not understood until quite recently.

[1] Members of Lepidostromatales closely resemble species of Multiclavula because these groups share a combination of clavarioid fruiting bodies and lichenized thalli.

[2][3] The group was first recognized as distinct on account of the small squamules (scale-like structures) that make up the thallus, and the genus Lepidostroma was created as a result.

[1][8] However, the photobiont of Lepidostromatales is chlorococcoid instead of coccomyxoid (which is the type found in Multiclavula),[8][9][10] making the photobiont-type a reasonable diagnostic feature for the group.

The three thallus types correlate with the current division of the group into three genera: All known members of the order are lichenized and grow on soil in tropical regions of Africa and the Americas.