The yellow-throated marten (Martes flavigula Boddaert 1785) is a medium-sized carnivore and a top predator in South Korea that is distributed throughout Western and Southeast Asia and Siberia in a wide range of habitats. In this study, we developed a panel of polymorphic microsatellite markers for M. flavigula by Illumina next-generation sequencing for investigation of population genetics. A total of 887 candidate microsatellite markers were identified and characterized from genomic sequences. By testing the markers in three individuals, we found 73 satisfactory microsatellite loci consisting of tri- or tetranucleotide repeats. We designed four multiplex panels of 33 microsatellite loci and applied them to 35 individuals from South Korea. The number of alleles and polymorphism information content per locus varied from 2 to 9 and from 0.164 to 0.841, respectively. The observed and expected heterozygosity per locus ranged from 0.143 (MF233) to 0.800 (MF339) and from 0.183 (MF233) to 0.871 (MF327) respectively. Nine of the 33 loci deviated significantly from Hardy-Weinberg equilibrium. We also found that at least 10 of the loci were transferrable to two other species of Mustelidae (Meles and Mustela sibirica). These markers can be applied to studies of genetic variation and population structure and can be useful for ex situ conservation and ecological monitoring by non-invasive sampling of M. flavigula populations.