Information system integration is an essential part of a collaboration between organizations un a single organisation's functioning. It is even more important in mergers and/or acquisitions, considered in this doctoral thesis as the context of information system integration. Despite the popularity of the merger un acquisition (M&A) strategy, studies of the results of these initiatives show that only half of them achieve the set goals. The main idea behind M&A is to create a new organization by combining several existing organizations. This organization must be able to achieve the goals stated for M&A, which could not be achieved by each of the merging organizations separately. This new organization is created by a transformation process, often called a post-merger integration (PMI). Successful information system integration is cited as one of the most important factors contributing to PMI success. Information system integration can be perceived as the sequence of integration decisions un decision implementation activities. In the scope of this thesis, integration decisions are perceived not only as a choice between possible information system integration options (decision-making) but also as a question about for which information system integration the option should be selected (decision identification). This doctoral thesis is focused on the problem that organizations new to PMI lack expertise in PMI information system integration, which is why in the scope of information system integration decision identification un decision making they are unable to achieve results comparable to the results of experts. The expertise is understood here as high level knowledge un skills, which support decision identification un decision making in scope of PMI information system integration domain. The following hypothesis is formulated: "Specialists without expertise in the PMI information system integration with the support method can achieve results comparable to the results of experts in the identification of groups of information systems to be integrated (identification of decisions) un analysis of integration options (decision making)". Accordingly, the main goal of the doctoral thesis is to develop support methods for informed identification of groups of information systems to be integrated un analysis of integration options in PMI initiatives. In order to achieve these goals, in the scope of this doctoral thesis, two support methods ̶ for the informed identification of groups of information systems to be integrated un analysis of integration options in the PMI initiatives ̶ were developed. Solutions included in the methods are rooted in requirements engineering, enterprise architecture, multi-criteria decision making, postmerger integration levels synchronization, postmerger contextual factors, un knowledge management research areas. Both developed methods are based on a concept of methodological support for PMI IS integration, which was developed in this doctoral thesis. For each of the methods a support tool was developed for a more convenient practical application of the method. The developed methods were validated through simulation, experimental evaluation un usability evaluation.