This paper examines methodological challenges throughout a cross-cultural case study on teacher work and practice and outlines the researcher's reflections on and responses to these challenges. Special education teachers working in Japanese and Australian special education settings shared classroom ecologies in that they worked with small groups of children including one or more with autistic spectrum disorders (ASDs). They also engaged with other educators about their everyday work. However, how they did their work differed within their multilayered cultural contexts: National (e.g., educational emphasis, curriculum approach), institutional (e.g., school emphasis, community of practice), and personal (e.g., classroom structures, personal experiences). Field research in these complex settings and data analysis of these two cases encountered boundary issues. The paper outlines how the researcher worked with teacher participants to solve problems together and how she employed their shared ecologies to create a structural framework to compare and contrast these culturally different cases. The need for slightly different methodological paths for investigating these cases will be discussed.