This species is here subdivided into four subspecies below. See under subsp. marginalis for the original species.

Although Wehmeyer (1926a) combined Diaporthe marginalis in Melanconis, he later (Wehmeyer 1941) argued that the conidia only differ from those of M. alni in depth of pigmentation and, therefore, reduced M. marginalis to a subspecies of the latter. In Europe, where, owing to Wehmeyer (1941), Melanconis on Alnus was always identified as M. alni, Petrak (1941) reported Melanconium dimorphum for the first time, described both conidial types, but still found it probable that Melanconium dimorphum was an abnormal form of M. sphaeroideum, the putative name of the asexual morph of M. alni. Kobayashi (1970) and Jensen (1984), however, were convinced that Melanconis marginalis should be treated as a species separate from M. alni, which is here confirmed phylogenetically. In addition, ascospores of M. marginalis are narrower, usually more oblong and symmetric than those of M. alni and appendages shorter, stouter and rounded or truncate at the ends, which swell and become diffuse in mounts.