Pet reptiles are gaining popularity among Saudi citizens but owners lack public health-associated awareness. Generally, the pet shops do not properly guide about reptile handling and health precautions. This study features molecular characterization of Salmonella isolates from pet reptiles to detect potential human pathogenic serovars. Previously identified five Salmonella sp. isolates from pet reptiles in private households were subjected to PCR amplification of 16S rRNA gene followed by Sanger sequencing and phylogenetic analysis. Sequencing confirmed all five isolates as Salmonella enterica subsp. enterica serovar Typhimurium. Different strains shared a common ancestor but were divided into different clades in various host species (snakes and lizards). All reptiles could be a potential source of zoonotic Salmonella spp. and multidrug resistance (MDR) of Salmonella can further worsen the situation. The feed, confined shared living spaces of multiple animals, environmental conditions, and pets’ interaction with wild animals could enhance the probability of Salmonella spp. occurrence in pet reptiles. This study necessitates the pet owners’ awareness regarding Salmonella spp. transmission routes and associated human health repercussions while keeping pet reptiles.