We describe eleven polymorphic microsatellite loci developed for Blera fallax using ‘next generation’ 454 whole genome shotgun sequencing, along with conditions for three multiplex PCR reactions. We tested allelic variation on forty B. fallax individuals from Scotland and Sweden. Allelic richness and expected heterozygosity were 3.03 (±0.274) and 0.391 (±0.057) respectively. The number of alleles per locus ranged from 2 to 6. We anticipate that these loci will assist conservation management by allowing the monitoring of translocated populations, estimating effective population size, and assessing population structure and dispersal in Scotland and across Europe.