Ebola Virus (EBOV) infection affects humans beings in the last four decades with the deadliest outbreak at 2015 in West Africa, leaving more than 10,000 deaths. The virus harms the liver of the patient when direct contact with contaminated body fluids or blood is occurred. L polymerase is one of the viral proteins responsible for the viral RNA replication. Inhibition of the viral polymerase succeeded is in stopping the infection of other viruses such as Hepatitis C Virus (HCV). National Center for Biotechnology Information (NCBI) protein database has 2123 sequences for L polymerase. In present research, the sequence and phylogenetic analysis are utilized to understand the non-redundant sequence coming from different countries. Based on the sequence similarity, the solved structure of vesicular stomatitis virus (PDB ID: 5A22) is used in this work to suggest the active site of the EBOV RdRp domain. Two newly released sequences (APT69557.1 and ALX33626.1 for the Sudan and Zaire, respectively) are based on the phylogenetic analysis, show interestingly a divert, mutation and distance from its subgroups suggesting a new emerged isoform of EBOV RdRp. The active site motif, GDN, would be targeted by polymerase inhibitors succeeded in other viruses to get stop the infection