The aim of the work is to search for loci of the genome of various types of foot-and-mouth disease virus (FMDV), characterized by the lowest variability, for use as genetic markers in the polymerase chain reaction (PCR) of virus identification. The nucleotide sequences of the genomes of FMDV of types A, Asia-1, C, O, and SAT (1, 2, and 3) were analyzed. When aligning the genomes of isolates of each type of virus, potentially conservative sites were identified. Comparing these loci, different types of the virus have one, the most conserved locus. Subsequent basic local alignment search tool (BLAST) analysis established the correspondence of the conservative locus to the FMDV genome, and primers and a probe were developed to amplify this locus.