Background: Antimicrobial Resistance is a major concern because a resistant infection may kill, and can spread to others, and imposes huge costs to individuals and society. The prevalence of MCR-1 resistance gene in Sudan possesses potential threat for treatment of patient especially when hospitalized. This study was implemented to determine the prevalence of MCR-1 Resistance gene in Khartoum state Hospitals in K. pneumoniae, isolates from clinical specimens using Polymerase Chain Reaction (PCR) technique. Methods: In this study, one hundred Klebsiella pneumoniae isolates from clinical specimens the study was (31%) were males, while (69 %) were females. There were aged from (17 to 40) years with (Mean = 27.4 and SD = 6.598). The isolated organisms were stored in 20% Glycerol Peptone Media. Samples were cultured and Re-identified using conventional methods. And tested to antimicrobial susceptibility test using Kirby baur disk diffusion Method. Results: 11% were Resistance for AST to colistin. then presence of MCR-1 gene was investigated by Polymerase Chain Reaction (PCR) technique. Out of 100 of Klebsiella pneumoniae Isolates, 4(4%) show positive MCR-1 Three of them from these 11% Resistance and only one from other 89 sensitive the data computerized and analyzed through SPSS 23. All statistical tests have done using chi-Square and the association of Colistin Resistance with MCR-1 gene were significant p-value (<0.05). The Colistin Resistance is an alarm from staff holders because it is considered as main treatment for ICU infections.