This paper analyzes border issues between Sudan and South Sudan, since the 2005 Comprehensive Peace Agreement . It also provides insight into the report of the Boundary and Demarcation Commission regarding the contested border areas such as (Jouda, Mount Almeqinas, Kaka Commercial Area, 14-mile area and Abyei). The paper is also attempts to study the impact that secession has had on population groups along the border lines. The paper found that border issues between Sudan and South Sudan cannot be resolved through arbitration, referendum or even demarcation. The border lifestyle and associated population density have produced a complexity that will continue beyond the next 100 years. This would only change in the event of a fundamental lifestyle shift in the societies on either side of the border. The resolution of flexible borders remains the only logical solution that can establish lasting peace and mutual trust among the tribes of the region.