This study is a series of Didactical Design Research in prospective analysis stage to comprehensively identify some obstacles in learning negative integer in order to capture how the learning process used by teachers and how the impact on students in understanding the concept of negative numbers. This research is a case study administered to seventh-grade students in one of the classes in a junior secondary school in Indonesia to investigate how the teacher managed the learning process of integers and identify students' thinking construction. Involving a mathematics teacher and 37 students, this qualitative study collected data from field observations, interviews and document review. The data were analyzed by the perspectives of learning obstacles based on Theory of Didactical Situation. Findings show how teacher describes the negative integers and the arithmetic concepts to the students and its contribution in causing misunderstanding on the students. Within the framework of epistemological obstacles, the result of this study is used as a basis for designing a learning program which can overcome problems related to teaching and learning of negative integers.