The caparari (Pseudoplatystoma tigrinum) is a widely distributed species in the Amazon Basin. It has a high market value and it is commonly consumed by the local population. In order to protect the species from possible overfishing, there is a need for a better understanding of the population diversity, since knowledge regarding its biology is scarce, which makes it difficult to monitor. Seven microsatellite loci (simple sequence repeats-SSR) for the species were isolated and characterized in 46 individuals which were sampled in four locations from the Madeira River, in the Brazilian Amazon. The number of alleles per locus ranged from three to eleven. The observed and expected heterozygosity ranged from 0,326 to 0,705 and 0,322 to 0,758, respectively. No linkage disequilibrium between pairs of loci was detected. The seven microsatellite loci were additionally used for inter-specific amplification in other four species of Pseudoplatystoma. Therefore, this study contributes to the first molecular species-specific SSR markers, which can be used as a new tool for estimating the genetic variability of P. tigrinum and has potential for application in population-related studies.