This article adopts the historical neo-institutional approach to analyse the dissolution of the Livonian Confederation and the ensuing reshaping of the Baltic region in the 16th-19th centuries. These historical events are employed to describe the post-bifurcation incorporation of a society in a different social system. Several inclusion models are identified. The centralised model suggests that the incorporated society reproduces the institutions of the incorporating society. Modified institutions are transplanted to the incorporated society within the quasi-centralised model, whilst only selected modified institutions are transferred within the autonomist one. The author analyses the mechanisms playing a part in state mergers and emphasises their dependence on the institutional environment of the incorporating society. For instance, a part of Livonia was incorporated in the Polish–Lithuanian Commonwealth (PLC) through transplanting PLC institutions, primarily political ones, to the newly acquired territories. To this end, a mechanism was developed to encourage cooperation from the nobility without further stratification. Sweden, however, acted on the autonomist model when incorporating Estland and Livland. Economic, political, and socio-cultural institutions, many of which were of hybrid type, were transplanted, whilst socialisation mechanisms and incentives applied to a wider section of the population. The Russian approach, which had at its core security considerations, combined autonomist elements (establishment of hybrid institutions in the new territories) and centralised components (propagation of Russian imperial institutions). The merger mechanisms included the creation of an Ostsee estate system and incentives for the higher estates coupled with repressions against commoners. Overall, the nature of state mergers and institutional transplantations depends on whether the incorporated territories have had a history of statehood, another significant factor being the degree of similarity between the institutions of the acquired territories and the metropole.