A set of 12 microsatellites was developed for a freshwater fish golden mahseer, Tor putitora. Golden mahseer is an endangered and endemic in mid-hill regions of South-Asian countries. Constructing a partial genomic library, we obtained 44 clones containing putative microsatellite motifs and 12 microsatellite with enough flanking sequence for primer designing. The number of alleles per locus ranged from 3 to 8 (mean 5.41), with a mean expected and observed heterozygosity of 0.68 and 0.66, respectively. Most of them were in Hardy–Weinberg equilibrium except TPM20a. There was no significant evidence for linkage disequilibrium between any pair of loci. These microsatellites were highly polymorphic (mean PIC 0.68) and will be useful for genetic variability and conservation genetics studies.