Tambaqui (Colossoma macropomum) is the South American freshwater fish with the highest aquaculture production levels in Brazil. Current production exceeds 150,000mt/year and accounts for close to 30% of all finfish cultured domestically. The species is at early stages of domestication, with initial efforts to stablish genetic improvement programs recently set underway. High fecundity rates (>300.000 larvae per spawning) associated with unsophisticated processes to establish and manage broodstocks have the potential to rapidly reduce effective sizes of captive populations. Therefore, practical contemporary tools to minimize inbreeding rates resulting from mattings between unknown close relatives are highly necessary. A database containing >2.5million SNPs identified in a previous high-coverage genome-wide sequencing study of pooled samples with complexity reduction for the species was analyzed to identify candidate SNPs. A total of 2,040 markers with estimated 0.45<MAF<0.5 and zero observed SNPs in flanking regions was identified. Additional filters to select 144 SNPs evenly spaced across all 27 chromosomes were applied. SNPType® assays were designed and used to test the 140 samples originally used for SNP discovery, including closely related species commonly used for hybrid production (Tambaqui=63, Pacu (Piaractus mesopotamicus)=23, Pirapitinga (Piaractus brachypomus)=48 and six known hybrids), with a Fluidigm EP1® system. Technical replicates were carried out to evaluate genotyping consistency. The best 96 markers were selected considering call rate, HWE and observed MAF. None of the tested markers were observed to be polymorphic in non-Tambaqui samples. Additional samples randomly collected from six different commercial broodstocks (n=188) were tested. Average observed MAF and Call Rate were 0.37 and 0.99, respectively. Estimated combined probability of exclusion was 9.9999999E-01. Kinship analysis of tested samples showed high levels of family-structuring within and between broodstocks. Management of broodstocks for production of fry for both grow-out, and broodstock establishment and replacement, considering obtained kinship estimates, will generate gains in productivity, minimizing losses caused by deleterious mutations and inbreeding depression.