Duikers are small ungulates that are widely distributed in African rainforests, but the information on genetic structure is scarce. We developed microsatellite markers using next generation sequencer which can reduce costs and time compared with the traditional methods. Tissue and fecal samples of blue duikers were collected in bushmeat markets and Moukalaba-Doudou National Park in Gabon, respectively. We prepared shotgun library using one tissue sample and sequenced using GS Junior (Roche). Microsatellite sequences were searched using MSATCOMMANDER from the shotgun data. Primer candidates were selected using PRIMER 3. We obtained 77,820 sequences and found 914 sequences with tandem repeats: 792 di-, 114 tri-, and 8 tetranucleotide microsatellites with at least 8, 7, and 7 repeats, respectively. Among them, 324 sequences contained suitable primer sites. We tested 25 dinucleotide and 5 trinucleotide loci using 3 tissue and 5 fecal samples. We successfully amplified target regions at 25 loci and selected 7 loci according to the number of alleles and heterozygosity. The average heterozygosity of these 7 loci was 0.797 with the range of 0.539-0.914. The probability of identity using these 7 loci was quite low (1.3 � 10^-9). These markers are useful for clarifying genetic structure of wild duikers.