The genus was circumscribed by the Dutch lichenologist Laurens Sparrius in 2009. Synarthothelium is distinguished from other genera in the Arthoniaceae by the presence of a thalline margin surrounding its reproductive structures (ascomata). While superficially resembling some members of the family Roccellaceae, such as Schismatomma and Mazosia, Synarthothelium differs in its ascus structure and larger spores. The asci are clavate (club-shaped) to globose (roughly spherical), similar to those found in Arthothelium (referred to as Arthothelium-type), and contain large ascospores.[3]
The genus shares some characteristics with Cryptothecia and Stirtonia, which also have large spores and similar asci. However, these genera lack distinct ascomata and have different thallus structures. Synarthothelium can be further distinguished from Arthonia, Arthothelium, and Synarthonia based on various morphological features.[3]
Another genus in the Arthoniaceae with a thalline margin is Amazonomyces, but it is strictly leaf-dwelling (foliicolous), has differently shaped spores, and produces abundant reproductive structures with very large conidia. The ascomata of Synarthothelium most closely resemble those of Arthothelium, but differ in having a thalline exciple, a carbonised excipulum, and non-muriform ascospores.[3]
The genus Paradoxomyces, while sharing some features with Synarthothelium, lacks a thalline margin and is known only as a lichenicolous fungus (growing on other lichens) without its own visible thallus or associated algae.[3]
Synarthothelium was originally classified tentatively in the family Arthoniaceae[4] before being placed as incertae sedis (uncertain position) in the order Arthoniales in 2016, because of a lack of molecular sequence data.[5]
