Many countries in the Baltic Sea basin have initiated enhancement programs for Baltic migratory sea trout, Salmo trutta L., to compensate for losses stemming from anthropogenic pressure that has resulted in the declining population abundance of this species. Regular stock enhancement has been conducted in Poland since the 1960s. Currently, over one million sea trout smolts are released into Polish rivers annually. In most Baltic countries, including Poland, stock enhancement depends on hatcheries producing material using spawners caught in native rivers. However, increasing difficulty obtaining spawners in recent years in Poland has meant that stock enhancement performed in the Vistula has been done largely with material obtained from broodstocks. Simultaneously, there is a lack of information regarding the proportion of wild and cultured sea trout in this river basin. This paper is a review of methods applied to identify individuals from natural and artificial sea trout spawning in rivers, and it proposes using genetic techniques as an alternative to traditional marking methods. A set of 13 microsatellite loci are proposed that are characterized by high selectivity. Using negative controls while simulating the assignment of parental pairs revealed that the number of loci in the set was highly significant and should not be reduced. This method could be useful in the proposed assessment of the proportions of wild and cultured fish in Polish rivers.