In theDrosophilaovary, developing germline cysts are encapsulated by somatic follicle cell epithelia and E-Cadherin localizes to the interface of these tissues. E-Cadherin mutants have been shown to have multiple defects in oogenesis. Therefore, it is difficult to determine E-Cadherin function on germline-soma interaction. In this study, we characterize E-Cadherin function, specifically focusing on germline-soma interaction. Unexpectedly, knockdown of E-Cadherin either in the germline or follicle cells results in excess formation of membrane protrusions at the interface of these cells, which leads to a cell-cell fusion and indicates that homophilic interaction of E-Cadherin is required for maintenance of the tissue boundary between these two adjacent tissues. The fate of follicle cells fused to the germline becomes compromised, leading to a defective individualization of germline cysts. We propose that homophilic interaction of E-Cadherin facilitates a barrier between adjacent tissues, demonstrating a unique model of cell-fate disturbance caused by cell-cell fusion.