This material presents the data used in the study "Rampant Interkingdom Horizontal Gene Transfer in Pezizomycotina? An Updated Inspection of Anomalous Phylogenies". The data is organized into three main directories: the DarkHorse software candidates (DH_analysis_result), the bibliographically recovered candidates of interkingdom horizontal gene transfer (HGT) (PUBMED_search_analysis_results) and the data used to reconstruct the Pezizomycotina species tree (Pezizomycotina_species_tree). The first two directories contain three subdirectories each, with protein inputs in genpept format, alignments after Gblock refinement in fasta format, and annotated phylogenetic trees in nexus format. These subdirectories are further divided into several directories according to the patterns described in Figure 1 of the main manuscript.