The taxonomic differentiation among lactic acid bacteria (LAB) using only phenotypic methods is inadequate. In the past, several phenotypic techniques have been applied in identification of different species of LAB from Nigerian indigenous fermented foods. In this study, two less-expensive and rapid molecular techniques were employed in the identification and differentiation of LAB species isolated from some Nigerian fermented foods: gari (cassava mash), fufu (cassava dough) and ogi (maize gruel) to avoid the common errors that are synonymous with the use of conventional methods. The size of the amplified products for the LAB species using universal primers fD1 and rD1 was about 1500 bp. The differentiation of the three predominant LAB, Lactobacillus plantarum, Pediococcus pentosaceus and Weissella confusa to species level was performed by intergenic transcribed spacer (ITS-PCR) and amplified ribosomal DNA restriction analysis (ARDRA) using three restriction endonucleases: HinfI, HaeIII and RsaI. In summary, the study demonstrated that the ARDRA and ITS-PCR analysis are simple, fast and efficient methods that can be used for the routine identification and rapid differentiation of LAB species which are often regularly used as probiotics, starter culture and biopreservative in fermented foods consumed since they are generally regarded as safe (GRAS). (C) 2016 Elsevier Ltd. All rights reserved.