Hepatitis C virus (HCV) is a global problem and the genetic diversity in non-Western countries  particularly in Egypt, where the highest prevalence of HCV is very important because of showing distribution of different HCV genotypes . This study aimed to  report phylogenetic analysis of hepatitis C virus isolates based on the 5` untranslated region (5`UTR) in Egyptian populations using 51 samples with high and moderate viral load , selected from different regions in Egypt. Samples were identified based on RT-PCR amplification of the 5` UTR. The data were confirmed by sequencing and phylogenetic analysis using Multiple Sequence Alignment to describe the similarities of different isolates of HCV.The results appeared a high level of genetic diversity of  genotype  4 with 90.2%  that  was commonly found with its subtypes ranged 4a (74.5%) ,4l (5.9%) ,4v (5.9%) and 4n (3.9%) while genotype 1 recorded 9.8% with its subtypes ranged 1a (3.9%) ,1b (2.0%) and 1g (3.9%).  Using Multiple Sequence Alignment of HCV isolates indicated high percent of similarities between different genotypes of isolates. The results obtained in this study provide a strong evidence for high percent of similarities between different genotypes of isolates obtained from different Egyptian regions.