The main objective of this paper was to decompose Total Factor Productivity Change (TFPCH) of cotton cultivars Barakat-90 and Barac(67)B in the Gezira scheme in 1991-2007, based on Data Envelopment Analysis Program (DEAP) Software Version 2.1, using model of input–oriented Malmquist indices Total Factor Productivity (TFP). This model could give meaningful results regarding technological and economic behavior relationship over time using balance panel data on Barac(67)B and Barakat-90 cultivars, Relevant secondary data were collected and analyzed to meet the stated objectives. This paper was aimed to decompose TFPCH into two components Technological Change (TECH) and Technical Efficiency Change (EFCH) and the latter was further divided into Scale Efficiency Change (SEFCH) and Pure Efficiency Change (PEFCH). The methodology allowed the recovery of various efficiency and productivity measures. The paper was mainly to answer the questions related to technical efficiency, scale efficiency and productivity changes. In the study on cotton cultivars, the innovation was improving up and down of TECH over time. Scale inefficiency was the main problem in efficiency analysis and mainly due to production operating at increasing returns to scale in Barac(67)B and Barakat-90 operating at constant return to scale. TFPCH was -1.3%, the contribution of EFCH was -1.6% and TECH was 0.30%, the main problem was efficiency change and this was mainly due to scale inefficiency, Barac(67)B contributed to this negative at an average annual rate -3.3%. This implying that the Barac(67)B was ailing due to efficiency change. The study has recommended, substantial improvement in knowledge about productivity and efficiency using scientific approaches, the scheme administration should take full advantage of Barac(67)B cultivar to be extensively grown, Barakat-90 requires further investigation benefiting from technological innovation, additional, improvement in agricultural processing to increase the value added, and the benefit of scientific breakthrough in agricultural science are also recommended.