Understanding how microsatellites are distributed in eukaryotic genomes is important to clarify the differential abundance of these repeats under an evolutionary scenario. We have concatenated data from 3165 DNA sequences of 326 Bivalvia species to search for taxonomic patterns of microsatellite distribution in genomic regions of markedly different functionality. Some microsatellite motifs in bivalves showed one of the lowest genomic densities observed among eukaryotes. Contrary to the expectation of a random distribution of microsatellites, they were overrepresented in introns (245 loci/Mb) compared to their frequency in exons (85 loci/Mb). Closely related species showed remarkable differences in microsatellite density suggesting species-specific properties as for mutation/repair efficiency on replication slippage. There was no evidence of a positive correlation between the density of microsatellites in intergenic DNA and the DNA-content. This research is relevant to better understand the forces shaping the distribution of microsatellites in the genome of bivalves.