Muyocopron species are associated with a wide variety of plant substrates worldwide and presently 57 species epithets are listed in Index Fungorum. Species in this genus form distinctive black, dull, rounded regions on the surface of plants and the genus is probably polyphyletic. The present study clarifies the phylogenetic placement of Muyocopron and related species, using fresh tropical collections from northern Thailand. Three Muyocopron species are characterized based on analyses of combined LSU and SSU sequence datasets. Phylogenetic analyses indicate that Muyocopron species form a distinct lineage with the Dyfrolomycetales and Acrospermales lineages. The new order Muyocopronales with three new Muyocopron species is introduced based on its distinct phylogeny and unique morphological characteristics. The taxonomy and phylogenetic relationships of tropical Muyocopron species are reappraised with suggestions for future work.