Foot and mouth disease (FMD) is a viral infection affecting ruminants and leads to great economic losses. Control and prevention have been a challenge despite the availability of vaccines. The causative agent exists in seven serotypes and is endemic in Kenya, with serotypes O, A, SAT (South African Territory) 1, and SAT 2 and having circulated in the recent past. This study was aimed at determining the current serotype diversity and serotype O variants during the study period. A cross-sectional study was conducted and a total of 267 epithelial samples were collected from animals during the disease outbreaks of 2019 and 2020. Antigen detection was performed using ELISA (Enyme-Linked Immunosorbed Assay). The negative samples were inoculated on LFBK(Line of Fetal Bovine Kidney) monolayer cells followed by a repeat ELISA for CPE(Cytopathic Effect) positive samples. The partial VP1 gene for serotype O samples was amplified and directly sequenced. The generated sequences were analyzed and compared with the vaccine strain. The prevalence of FMDV was 65.9% (176/267) and serotypes SAT 1, O, SAT 2, and A in the order of decreasing prevalence were circulating. Serotype O viruses analyzed belonged to the EA 2 against the EA 1 vaccine strain in use. For better control of the disease, this study recommends close monitoring of the circulating serotypes and topotypes, and, regular vaccine matching to ensure vaccine effectiveness.