Tomato is one of the most important crops worldwide. DNA barcoding is a molecular based method that has been successfully used for species identification, but a few studies have used this method for cultivated varieties identification. The aim of this study was to test the utility of DNA barcoding for the identification of five local salt tolerant tomato varieties and two commercial varieties. To assess the genetic diversity of tomato varieties, the non-coding plastid trnH-psbA intergenic spacer and three plastid regions (rbcL, rpoC1, rpoB) were used. Based on the sequence variation of the trnH-psbA barcode, three haplotypes were detected among the seven tomato varieties. A neighbor-joining tree was generated and separated the local tomato varieties from the commercial varieties into two distinct clusters. We found very low levels of variation in the chosen plastial markers, but additional markers could be tested in order to assess the utility of DNA barcodes in tomato varieties identification.