One of the most significant natural disasters in South-east Asia, is flooding. In Malaysia, for instance, Iskandar Malaysia region as a rapid urbanizing context located in southern peninsula has been affected by several flood events during last decade. Severe rainfall, natural situation, new unplanned developments and insufficient drainage systems mad the situation more considerable. This study seeks to address the crucial variables which contribute to the risk of flooding based on the characteristics of the region and develop a GIS-aided urban flood susceptibility map. The methodology emphasizes on uncertainty and multi-criteria which contribute to the risk of flood and increase the risk. As such, the Fuzzy logic, Multi-criteria ranking and Weighted Linear Combination (WLC) methods in Geographic Information System (GIS) are used to achieve the objectives. Distances from main stream, river and discharge channels, as well as other variables such as elevation, slope and land use are recognized as effective variables within the region. Final susceptibility map indicates that around 658 km 2 out of 1,614 km 2 within the region is under the high level of flooding risk. Different districts within the region include Pulai, Senai- Kulai, Tebrau and Johor Bahru can be considered as areas with a high risk of flooding. Natural and man-made situation influence the level of risk in each area. Generally the southern part of the region has a high level of risk as the consequence of conjunction between location of stream, lowland and land use type. Finally the situation in 2025 is investigated based on the proposed plan for 2025.