The setup of a flexible and cost-effective 96-SNP assignment panel to be used in Pekin duck (Anas platyrhynchos), Muscovy duck (Cairina moschata) and their mule duck hybrid, is presented. SNP were selected on the available 600K array in ducks. This SNP array is made of two libraries (one for the Muscovy duck, the other for the common duck which encompasses the Pekin duck), the intersection of which, after a preliminary elimination on the primer length, contained only 399 SNP that were considered a starting point to obtain a final list. A first step was to obtain a list of 192 SNP, based on technical properties, using a reference set of 600K genotypes from commercial lines. In a second step, to obtain the final 96 markers, a subset of the previous reference set was combined with genotypes from 134 Pekin and 128 Muscovy, which were the parents of the experimental populations to assign. Assignment rates were 99%, 96% and 88% in the mule, Pekin and Muscovy populations respectively. The lower-than-expected assignment rate in the Muscovy population was due to the absence of 16 parental samples. Availability of an effective and affordable assignment panel was deemed necessary after switching from a system where breeders are housed in individual cages to a system where females are housed and inseminated in groups. In the latter case, a factorial mating design replaced the hierarchical design, common in poultry. This new design impacted the population structure, creating more sire x dam combinations, offering possibilities for a better estimation of non-additive genetic effects, which could prove relevant in the foie gras sector. Finally, a list of 135 markers resulted from this study that could be used to build an efficient 96 SNP panel for any local or commercial population.