Horizontal (or lateral) gene transfer (HGT) is frequently observed in prokaryotes and until recently was assumed to be of limited importance to eukaryotes. However, there is an increasing body of evidence to suggest that HGT is an important mechanism in eukaryotic genome evolution, particularly in unicellular organisms. The mechanisms of HGT in fungi are not fully understood however, a number of possible mechanisms viz., conjugation like transfer, anastomosis and HGT mediated by selfish genetic elements including mycovirus, plasmid and transposons have been reported. Comparative fungal genomic analyses have shown the importance that HGT plays in the evolution of fungi. The transfer of individual genes, gene clusters or entire chromosomes can have significant impacts on niche specification, disease emergence or shift in metabolic capabilities. Bioinformatics-based methodologies are commonly used to locate HGT in fungal genomes and investigate the possible mechanisms involved in transferring genetic material laterally into fungal species.