Brown trout (Salmo trutta) is a salmonid species with a high socio-economic value related with recreational fishing. Because of that, stocking programs have been developed in many populations, although they have focused on resident populations. To explore which factors promote migratory behaviour when implementing stocking actions, 28 brown trout artificial crosses were carried out in a noncommercial hatchery, and the returning success of their offspring was further evaluated. Return rate was examined according to male phenotype (anadromous versus resident), mean egg size, parents’ similarity at major histocompatibility complex (MHC) class II β-gene, and stocking procedure. At the end of the experiment, 35 of the captured returning adults (9.4%) belonged to 14 of those crosses. Return success shows a significant effect (p = 0.0016) by parental MHC similarities, stocking procedure, and male phenotype. Our results indicate that planting fertilized eggs in nursery areas of the river, together with the selection of anadromous males as brood stock and mate pairs with higher similarity at the MHC locus, can be an appropriate option to increase the migratory part of trout populations. In addition, nursery areas can allow an important decrease in the cost per stocked individual, being 32 times less expensive than the cost per hatchery-reared individual.