Rodents are one of the most abundant and successful mammals on the planet. The rats harbor the metacestode stage of Hydatigera taeniaeformis serving as the intermediate hosts, whereas cats act as definitive hosts of the parasite. The incidence of the larval stage in rats has been documented in various regions of the world. To best of our knowledge, the mainstream studies on the genetic diversity of H. taeniaeformis are based on the cox1 gene which precludes an in-depth analysis of genetic variation in the parasite. To provide insights about nad1 gene-based genetic variation, in continuation of our previous work, we thereby in this study report H. taeniaeformis infection in the urban murine population from the Faisalabad district of Pakistan and presented genetic polymorphism using the nad1 gene. Out of 38 isolates investigated in the study, a total of 13 haplotypes were found with high haplotype diversity (Hd = 0.909), while the nucleotide diversity was found to be 0.02340 in the study population. The neutrality study found a significant level of nucleotide polymorphism, indicating a rise in low-frequency polymorphism, which might be attributed to global population growth of the parasite. Construction of phylogenetic comprising isolates from Kazakhstan, Finland, Turkiye, Canada, Germany, France, and China revealed that Pakistani isolates of H. taeniaeformis are distinct and formed a separate cluster. Further research utilising full-length multiple mitochondrial genes is required to understand the molecular epidemiology of H. taeniaeformis on the global scale.