In the age of globalization, the number of foreign nationals living in Japan is growing and their composition is diversifying rapidly. It has also been suggested that the diversification of migrants is a more complex phenomena than mere multi-nationalization, and concepts capable of understanding various aspects of foreign populations, such as super-diversity, have been proposed. The process of the diversification of foreigners has also been addressed in previous studies on Japan, although research subjects are usually limited to economically driven and systematic migrations. Applying the perspective of super-diversity allows us to also focus on different groups and to critically reconsider the assumptions on ethnic groups as the most obvious and unproblematic units of research and integration. In this paper, I focus on the case of Czechs and Slovaks in Japan. This case represents not only the growing diversification of foreigners in Japan, but in this case I also attempt to scrutinize the assumed natural inclination toward ethnic group formation. A small scale questionnaire and 13 in-depth interviews were conducted. Analyses of egocentric social networks based on interviews were used for the identification of social integration patterns and the role of ethnic peers or groups within the everyday life and survival strategies adopted by the subjects. The results show that the migration patterns of Czechs and Slovaks to Japan are more individualistic and less driven by economic factors then in the case of previously studied migrant groups in Japan. The subjects do not tend to naturally gravitate toward their ethnic peers and do not attach great importance to ethnicity as the primary criterion for social activities in their daily life, nor do they deny their ethnic identity. However, this particular integration pattern does not result only from their low numbers, but also the specific character of their migration and its effect on the transformation of the capital they possess.