A Gram-positive, small coccus-shaped lactic acid bacterium, strain LMG 23999(T), was isolated from Argentinean wheat flour. 16S rRNA gene sequence analysis revealed that the phylogenetic position of the novel strain was within the genus Pediococcus, with Pediococcus stilesii, Pediococcus pentosaceus and Pediococcus acidilactici as its closest relatives (97.7, 97.3 and 96.9 % gene sequence similarity, respectively). Fluorescent amplified fragment length polymorphism fingerprinting of whole genomes and whole-cell protein electrophoresis confirmed the unique taxonomic status of the novel strain. DNA-DNA hybridizations, DNA G+C content determination, comparative sequence analysis of the pheS, rpoA and atpA genes and physiological and biochemical characterization demonstrated that strain LMG 23999(T) (=CCUG 54535(T)=CRL 776(T)) represents a novel species for which the name Pediococcus argentinicus sp. nov. is proposed. Multi-locus sequence analysis based on pheS, rpoA and atpA genes was found to be a suitable method for the identification of species of the genus Pediococcus.