Melanconis is a monotypic genus in Melanconidaceae and mostly restricted to hardwood trees in Betulaceae, as endophytes and plant pathogens. During a routine forest pathogens investigation of canker disease in China, some melanconidaceous fungi were observed on Betula spp. with various symptoms. The primary objective of the present study was to identify species of Melanconidaceae associated with canker and dieback of Betula spp. in China. In the present study, we investigated 45 isolates using morphology and multi-gene phylogenetic analyses based on the internal transcribed spacers (ITS), nuclear large subunit rDNA (LSU), RNA polymerase II subunit 2 (rpb2), translation elongation factor 1-α (tef1-α) and β-tubulin (tub). Three melanconidaceous taxa were identified: Melanconis betulae sp. nov., M. itoana and M. stilbostoma. This is the first phylogenetic study evaluating species of Melanconis associated with canker and dieback disease of Betula spp. in China, resulting in the description of a novel species and the report of M. itoana as a new record.