The first microsatellite primers are described for the mayfly family Baetidae (order Ephemeroptera). Seven polymorphic loci were isolated and characterized for the species Baetis rhodani from two enriched genomic libraries. A total of 183 individuals were genotyped using these loci. Allelic diversity was high for all loci, and observed heterozygosities ranged between 0.382 and 0.772. A heterozygote deficiency was detected in some loci, suggesting the presence of ‘null’ alleles.