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Paralogous genes represent well-known problem in taxonomy that uses molecular features as the indispensable tool for delineation of taxa.Incongruent phylogenetic trees and incorrect taxonomic conclusions can result from mixing of paralogous genes in taxonomic studies.Beta-tubulin (benA), ITS rDNA and RPB2 all represent important loci in fungal taxonomy and the examples of incorrect use of their paralogues are presented.