Filamentous microbes that form highly developed symbiotic associations (ranging from pathogenesis to mutualism) with their hosts include fungi, oomycetes and actinomycete bacteria. These organisms share many common features in growth, development and infection and have evolved similar strategies for neutralizing host defense responses to establish symbioses. Recent advances in sequencing technologies have led to a remarkable increase in the number of sequenced genomes of filamentous organisms. Analysis of the available genomes has provided useful information about genes that might be important for host infection and colonization. However, because many functional similarities among these organisms have arisen by convergent evolution, sequence-based genomic comparisons will miss many genes that are functionally analogous. In the absence of sequence similarity, annotating genes with standardized terms from the Gene Ontology (GO) can facilitate functional comparisons. Here, we review common strategies employed by filamentous organisms during colonization of their hosts, with reference to GO terms that best describe the processes involved.