We isolated and characterized microsatellite loci for the red-crowned crane (Grus japonensis) from a microsatellite-enriched database, which was obtained using high-throughput sequencing technology. We designed primer sets for 445 microsatellite loci and after initial screening, 34 loci were genotyped in 31 red-crowned cranes. The number of observed alleles ranged from 3 to 10. Observed and expected heterozygosities ranged from 0.197 to 0.935 and 0.453 to 0.887, respectively; the mean polymorphic information content was 0.663. Loci Lia10943, Lia60455, Lia48514, Lia62171, Lia1059, and Lia5286 deviated from expectation of the Hardy-Weinberg equilibrium; however, significant linkage disequilibrium was not observed among the 34 loci. Using these 34 markers, we successfully completed parental identification for 19 cranes. The probability of exclusion for 7 selected loci (Lia271333, Lia3745, Lia11091, Lia45761, Lia16468, Lia21909, and Lia22355) was >0.9977 and analyses with more loci increased the combination efficiency. These 34 markers were also proven to be efficient for individual identification. We recommend that this marker system be used in the systematic control of pedigree management and future genetic variation studies of red-crowned cranes.