<p>We are honored and privileged to edit this Special Issue Fungal Taxonomy Phylogeny and Ecology: A Themed Issue Dedicated to Academician Wen-Ying Zhuang. In this Special Issue we are pleased to publish a comprehensive assemblage of 23 papers covering fungal taxonomy phylogeny and ecology in which 76 new taxa from a broad taxonomic group and different ecological habitats are reported.</p>