Undoubtedly, information security is one of the major factors in banking sector. Importance of achieving specific level of security becomes dramatically more crucial for customers and stakeholders when banks make use of electronic systems. In this vein, this study provides insights into assessment of information security diagnosis in e-banking in Iran. The present study is practical from the aim point of view as well as descriptive and survey from the nature and methodology aspects. The research sample size is consisted of 150 persons among managers, specialists and experts in Tejarat bank’s branches of Isfahan during the years 2014 which is opted using random sampling method. Having analyzed collected data using Structural Equation Modeling (SEM), paired sample T-test is employed to conduct a gap analysis between current (As-Is) and future desired (To-Be) states of information security in four dimensions including confidentiality, integrity, authentication and availability . Finally, in order to enhance the security level in e-banking of Isfahan Tejarat bank’s branches, some recommendations are presented.