Turkey and Israel have been strategic partners since the 1990s. Yet, there has occurred a deep crisis between the two countries, particularly since 2009, but the beginning of the deterioration in bilateral relations dates to the early 2000s. Today both countries designate each other as opponents despite the history of a strategic partnership. What are the reasons for this radical shift in the Turkish–Israeli relations? How might the stalemate in the relations be explained? This study analyses the rupture in the bilateral relations, particularly on the recent events that paved the way for a rupture and stalemate and evaluates it via three levels of analysis laid by Kenneth Waltz. The study argues that bilateral relations have taken shape at three levels in different times and that the deterioration and amelioration of the bilateral relations hinge upon the identity and ideology of the leadership at the individual level, domestic factors at the state level, and structural factors at the systemic level. In this regard, it seeks to reveal which of the levels of analysis are in play in the determination of bilateral relations since 1948.