Foot and mouth disease (FMD) is a contagious disease of cloven-hooved domestic and susceptible wild animals. Repeated FMD cases are reported annually throughout the country despite vaccinations being carried out. This has hampered livestock industry development in Kenya due to production losses and that of trade. This study was conducted to investigate if there is a mismatch between the field strains and the vaccine. The study was conducted on 110 epithelial tissues submitted in the year 2019 and 2020 to Foot and Mouth disease laboratory, Embakasi for screening. The samples were collected from outbreaks and suspected clinical cases of FMD in cattle from different counties in Kenya for virus isolation, serotype identification and genetic characterization. All samples (n = 110) exhibited cytopathic effect on infected BHK-21 cell and the viruses were isolated. Serotype A (n=4), SAT 1 (n= 69) and SAT 2 (n= 37) were identified by antigen detection ELISA. Of the total 30 samples selected, 25 were confirmed positive by RT-PCR. Phylogenetic analysis of the isolates VP1 sequences were used to assess the genetic relatedness with the vaccine strain and other viruses retrieved from GenBank. The analysis showed that type A viruses belonged to the genotype VII (G-VII) within the AFRICA topo type. The viruses were closely related topo type A vaccine strain AK5/80 with 99.5%99.8% nucleotide similarity. SAT 1 field isolates were closely related to the vaccine strain SAT1/T155/71 and had 99.7% - 99.9% identity with the vaccine. There was a similarity index of 99% - 100% between all the isolates and the reference vaccine strain in the country and all the isolates clustered together with their respective isolates on the tree. This shows there isn’t much difference between the field strains in the current study and the vaccine strains. Therefore, there is a need to re-look at other factors which may influence vaccine efficacy including vaccine xvstability, vaccination intervals and whether serotype O is similar to vaccine and or not to come up with effective vaccine strategies

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