Tambaqui (Colossoma macropomum) represents the most important neotropical freshwater fish used in aquaculture from South America, whose production is concentrated at low latitudes (close to Equator 0º) where the water temperature is warmer. Understanding how selection shapes genetic variation and the level of genetic structure in farmed populations is of paramount meaning in evolutionary biology. High-throughput sequencing to generate genome-wide data for non-model species allows determining the genomic basis of adaptation to local or farmed environmental conditions and uncovering genes that control phenotypes of interest. The present study aimed to detect genomic selection signatures and to analyze the genetic variability in farmed populations of tambaqui from South America, using SNPs markers obtained by double-digest RAD-sequencing (ddRAD-seq) technique. Initially, about 199 tambaqui breeders were genotyped from farmed populations of different locations (placed in Brazil, Colombia and Peru), a wild population (Amazon River, Brazil) and the base population of a breeding program (Aquaculture Center, CAUNESP, Jaboticabal, SP, Brazil). Observed heterozygosity (H_o) and expected heterozygosity (H_e) values ranged from 0.081 to 0.248 and from 0.206 to 0.270, respectively. Significant genetic differentiation was detected by global F_ST analyzes on SNP loci (F_ST = 0.060, p-value < 0.050). Different population groups were identified, relating farmed populations from Colombia and Peru that are differentiated from Brazilian ones. Several regions were identified under positive selection, particularly harboring genes of significance to aquaculture environments and suggesting local adaptation to stress under different environmental conditions. Genomic studies focusing on better knowledge of the genome in farmed populations of tambaqui are considered essential for aquaculture, mainly to provide in-depth understanding of the evolutionary history and resources for the development of breeding programs.