This study revealed how students’ understanding of negative numbers and identified their difficulties related with the concept of integer and its counting operation as part of identifying epistemological obstacles about negative numbers. Even though teachers have explained counting operation procedure of integer, but there was concept misunderstanding among students. The concept difference between what was comprehended by respondents in their learning process and knowledge science has resulted in wrong perceptions about the negative numbers. In this article, the authors explained how these misunderstanding in concepts occurred among students and how these ideas were expressed by the students in solving the problem which was related with counting operation of negative integer. This study was part of Didactical Design Research using qualitative approach in negative number learning by involving 96 students of 7th grade as participants in three different schools. This study showed some difficulties by the student to understanding negative numbers in terms of prerequisite knowledge, understanding concepts, procedures, principles and problem solving.