The current pace of whole genome sequencing has made it almost trivial to produce nearly complete fungal sequences.  This now gives us the ability to perform whole genome comparisons of fungi to investigate biological questions and genome evolution.  To this end, syntenic regions between Trichoderma reesei and four other filamentous fungi (Fusarium graminearum, Neurospora crassa, Magnaporthe grisea and Aspergillus nidulans) were identified.  An algorithm was designed that takes homologs from two fungi and places them side by side, optimizing homolog density, and minimizing gaps between homologs and the number of homologs in a syntenic region.  As would be expected, the percent coverage of synteny between T. reesei and the other four ascomycetes declines with time since the last common ancestor, with F. graminearum having the highest synteny and A. nidulans  the lowest.  This approach enabled the identification of regions in the T. reesei genome that were conserved in multiple genomes as well as highlighting regions of the T. reesei genome that have changed dramatically.  Finally, for genes within these highly conserved regions and for the gaps, GO terms and Enzyme Commission codes were assigned. These results were used to assess the possibility that there is selective pressure to force genes that are in the same biochemical pathway, have similar function or are involved in similar processes to maintain or gain proximity.