Simple sequence repeat (microsatellite) loci in coffee were identified in clones isolated from enriched and random genomic libraries. It was shown that coffee is a plant species with low microsatellite frequency. However, the average distance between two loci, estimated at 127kb for poly (AG), is one of the shortest of all plant genomes. In contrast, the distance between two poly (AC) loci, estimated at 769kb, is one of the largest in plant genomes. Coffee (AC)n microsatellites are frequently associated with other microsatellites, mainly (AT)n motifs, while (AG)n microsatellites are not normally associated with other microsatellites and have a higher number of perfect motifs. Dinucleotide repeats (AG) and (AC) were found in ATrich regions in coffee. Sequence analysis of (AC)n microsatellites identified in coffee revealed the possible association of these repeated elements with miniature inverted-repeat transposable elements (MITEs). In addition, some of the evaluated SSR markers produced transposon-like amplification patterns in tetraploid genotypes. Of 12 SSR markers developed, nine were polymorphic in diploid genotypes while 5 were polymorphic in tetraploid genotypes, confirming a greater genetic diversity in diploid species.