Proliferative kidney disease (PKD) caused by the myxozoan parasite Tetracapsuloides bryosalmonae is a severe parasitic disease of salmonid fish. Estimates of genetic variation in parasite populations across Europe are currently lacking. We developed the first polymorphic microsatellite markers for T. bryosalmonae using Illumina MiSeq sequence data derived from genomic DNA. Twelve polymorphic loci were identified from 24 tested loci. Allelic variation was low at most loci, ranging from 2 to 6 (average 3.0). The markers developed here are expected to be useful in future genetic studies of T. bryosalmonae, aimed at further understanding the dispersal of the parasite, host-parasite relationships and the epidemiology of PKD.