An overview of the character of microsatellites in 14 fungal genomes was obtained by analyzing databases containing complete or nearly complete genome sequences. Low GC content, rather than genome size, was the best predictor of high microsatellite density, although very long iterations of tandem repeats were less common in small genomes. Motif type correlated with %GC in that low-GC genomes were more likely to be dominated by A/T-rich motifs, and vice versa, although some exceptions were noted. The experimentally useful dinucleotide and trinucleotide arrays were analyzed in greater detail. Although these varied in sequence and length among fungal species, some that are likely to be universally useful were identified. This information will be useful for researchers wanting to identify the most useful microsatellites to analyze for the fungi included in this survey and provides a platform for choosing microsatellites to target in fungi that are not yet sequenced.