The multiethnic composition of local communities is a common phenomenon in modern societies. There are numerous examples of ethnic groups living peacefully side by side, irrespective of cultural diversity, symbolic, political and economic characteristics. However, it must be recognized that cases in which the differences are converted into latent and manifest forms of tensions and conflict are easy to find. The present paper consists of two parts. In the first part the theoretical and methodological dilemmas in the research of ethno-national identification and ethnic conflict are discussed. The starting point in the paper is a general assumption that the conflict (or peaceful) outcomes in multiethnic areas are associated with the complex dynamics of ethno-national identification. In methodological terms, the author argues for an integrative approach in which quantitative methods (such as surveys and content analysis) in the research of ethno-national identification should be combined with qualitative research methods (interviews, discourse analysis, oral history). The necessity of an integrative approach is advocated in the second part of the paper that presents the most important results of empirical studies of ethno-national identification, which the author conducted in more than a decade in multiethnic areas of Croatia and Bosnia and Herzegovina. Starting from the concept of social integration, it focuses on the interaction between two groups of factors affecting the ethno-national identification. The first consists of structural features of communities that are primarily determined by the impact of social institutions. The second relates to the activities of different social actors operating on national, regional and local levels. The results of quantitative research show that there are significant differences in the openness of ethnic boundaries and trust in social institutions between conflict areas and the peaceful ones. Nevertheless, quantitative analysis fails to explain the subtle interrelationships between and within areas of ethnic conflict and those of ethnic peace, especially when it comes to the complex action of social actors such as representatives and coalitions of political, cultural, religious and entrepreneurial elite groups at national and local levels. The complex dynamics of ethno-national identification at the local level necessitates the additional use of qualitative methods, which, despite their subjectivity and shortcomings, can substantially contribute to a better understanding of the social process of construction of ethnic identity and ethnic conflict.