Aquaculture is presently the only sustainable way of enhancing sturgeon caviar production as the use of wild stocks is banned throughout the world. Hence sustainable management and efficient genetic improvement of domesticated populations are major challenges for the development of farmed caviar. We estimated genetic parameters of caviar yields and quality traits (size, color and firmness) in the polyploid Siberian sturgeon A. baerii, one of the major sturgeon species farmed for meat and caviar worldwide. This study was performed in commercial breeding conditions, where two factorial mating plans were created to produce 77 families. Larvae were pooled at hatching and reared in common environment until the age of caviar production. We phenotyped 494 females, which were successfully assigned to their parents with microsatellite markers using a newly developed software, designed to manage genotypes with varying ploidy levels, up to 8 N. The genetic parameters were estimated using heteroscedastic multi-trait BLUP animal models. Heritability of body weight, ovary weight, caviar weight, caviar (egg) size, caviar yield, caviar firmness and caviar color were moderate to high (0.13 to 0.66) depending on the trait. Moderate negative genetic correlations were estimated between growth and caviar yields (−0.28 to −0.37) while genetic correlations between caviar (egg) size and caviar yield were more negative (−0.70 to −0.76). These results provide favorable grounds to improve the efficiency of farmed caviar production by selective breeding.