The aims of this thesis included identifying ways to mitigate the economic losses of the commercial fishery in the Gulf of Bothnia resulting from fishery regulation enforced to protect wild Atlantic salmon stocks, the recent decline in survival of hatchery-reared salmon, and the dramatically increased seal-induced catch and gear damage. In addition, these solutions should facilitate safeguarding the recently-recovered wild salmon stocks and seal populations. Other goals included adding to and updating basic knowledge on the effects of increased seal populations, migrating salmon stocks, the coastal trap-net fishery, and their interactions. Seal-induced damage to the commercial fishery was found to be a significant problem throughout the Gulf of Bothnia. Catch and gear damage varied considerably among regions, fishing periods, target species and trap-net models. The regional patterns in seal-induced damage depended on the number of seals in the region and the type of gear, which is strongly associated with the netting materials. Strong and thick materials are more resistant to the attacks of hunting seals. Finer materials and larger mesh sizes that entangle fish are most prone to seal damage. Besides careful selection of the netting material it is also possible to markedly reduce damage by appropriate gear modifications. Three modified trap-net models showed promising results in terms of seal protection, with the pontoon trap being the most successful design. The total size of the spawning salmon population in the Gulf of Bothnia was c. 230 000 in the first two years of the 2000s. The proportions of wild salmon and hatchery-reared salmon, however, appeared to markedly change between years. The survival rate of cultured smolts seems to be considerably lower than that of wild smolts. Large variation in the returning migration patterns and run timing of salmon was found between sea age groups, stock components, and among and within regions. Run timing estimates revealed that the temporal regulation effectively safeguards the wild salmon, but, at the same time, a substantial proportion of the reared salmon escape the coastal fisheries in different regions. The likelihood of survival of wild salmon captured with trap-nets and then released was high, and the cumulative mortality even after several capture-and-release events was estimated to below. Trapnet capture and release did not lead to considerable changes in the normal migration behaviour of Atlantic salmon. This result suggests the potential for a selective harvesting strategy; a system where exploitable (e.g. hatchery-reared fish) and safeguarded (e.g. wild vulnerable stocks) fractions of a fish population complex could be separated in a mixed-stock fishery. However, before introducing a practical and successful selective trap-net fishery, several preconditions should be fulfilled.