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Salmonella spp is the main cause of foodborne salmonellosis that is considered a public health threat all over the world. The robust usage of antibiotics in Egyptian poultry farms resulted in increasing the prevalence of multi-drug resistant Salmonella enterica. In this study, the authors identify five multi-drug resistant Salmonella enterica serovars. Multidrug-resistant characteristics of these isolates were detected. The taxonomic evidence of these isolates was investigated based on 16S rRNA gene sequence and pairwise sequence alignment between the isolates' sequence and the nearest sequences in the database. In silico restriction maps and phylogenetic trees were also constructed. The obtained sequences were deposited in the database under accession numbers MW311328.1, MW311371.1, MN820824.1, MN822653.1 and MW310702.1 for Salmonella enterica subsp. enterica serovar Enteritidis strains EG.SmE1, EG.SmE2 and Salmonella enterica subsp. enterica serovar Typhimurium strains EG.SmT1, EG.SmT2, EG.SmT3, respectively. The five Salmonella isolates in this study showed multi-drug resistant characteristics. Salmonella Typhimurium isolate EG.SmT3 revealed resistance to more than five antibiotics. Results of pairwise sequence alignment, restriction maps and phylogenetic tree confirmed the close relationship between S. enteritidis isolates (EG.SmE1, EG. SmE2) and S. typhimurium isolates (EG.SmT1, EG.SmT2). However, the other S. typhimurium isolate (EG.SmT3) revealed the lowest identity ratio (98.6%) with the nearest sequence. The relative divergence of this isolate could be attributed to proposed mutations as a result of the vigorous use of antibiotics in Egyptian poultry farms.