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ABSTRACT The Unionidae are among the most endangered fauna in the world and globally in decline. They are particularly vulnerable to habitat loss and fragmentation, susceptible to flow, pollution and climatic disturbances and introduction of invasive species. Despite their well-recognized ecological and conservation importance, there is a surprising lack of genomic resources currently available for European species., The aim of this study was to develop and characterize microsatellites for the near threatened freshwater mussel, Potomida littoralis using 454 sequencing., In order to improve genotyping throughput as well as cost-effectiveness, two multiplex-PCR reactions were designed to amplify 16 new loci. All the new 16 microsatellites were successfully combined in two multiplexed PCR with the number of alleles ranging from 2 to 25 per locus (with a mean of 10), confirming the utility of the new markers., The new genetic markers can therefore be used for studying the population genetic structure and evolution of this species, e.g. to examine current levels of genetic variability within and between populations and thus to contribute to conservation and management. Copyright © 2013 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]