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The objective of the present work was to develop species-specific microsatellite markers for P. scalare and to analyze the diversity and genetic structure of a wild population, from the Amazon River, and three commercial stocks (common, marble, and clown morphological variants), from farmers in Vieras-Minas Gerais. Through microsatellite-enriched genetic libraries, 11 microsatellite markers with adequate amplification patterns were characterized. Population genetic analysis identified eight polymorphic loci that generated 66 alleles ranging from two alleles (PSCA1B3) to nine (PSCA2H1). The polymorphic information content ranged from 0.031 to 0.827. High genetic differentiation was observed between the wild population and the stocks, and moderate differentiation between the three stocks. Deviation in the Hardy-Weinberg equilibrium was observed in one locus in the wild population, in five loci in the common morphological variant, in two in the marble, and in two in the clown morphological variant. Bayesian analysis of genetic structure revealed the existence of two clusters, one represented by the natural population and the other by the stocks. The developed microsatellite markers serve as a tool for the analysis of diversity and genetic structure and conservation studies of P. scalare.