Iran-Syria alliance has been one of the significant events in the Middle East in the 1980s and 1990s. Despite their differences in language, race, religion and political structure, they have developed a strong alliance which has had profound effects on the region. This paper deals with two questions: First, why was this alliance established and maintained from 1979 to 2000? And second, how has it affected the regional balance of threat during that period? It is hypothesized that alliance between these two countries was developed to balance out threats posed by the common regional threats i.e. Iraq, Israel, and the US in the 1980s as well as the US, Israel, Turkey, and Iraq in the 1990s. Library and the Internet were used as two resources of gathering data and an explanatory method was employed in this study. Based on the study and analysis conducted, according to four criteria proposed by Stephan Walt in his Balance of Threat Theory, it was found that Iraq, Israel, and the US in the 1980s and the Israel, Turkey,And Iraq in the 1990s, were the major reason of the alliance formed between two countries and maintained from 1979 to 2000.