The mpox virus (MPXV), which is an emergent orthopoxvirus with zoonotic transmission capability, represents a growing public health threat on a global scale due to the recently reported outbreaks in multiple countries after 2022. In view of the rising prevalence of genetically heterogeneous strains, such as Clade I and Clade II, there has been a growing research focus on the molecular aspects of pathogenesis, evolution, transmission, and epidemiology of MPXV clades. The current review focuses on the genome structure, mutations, viral fitness, immune evasiveness, and human-to-human transmission rate associated with MPXV clades. The comparative pathogenicity between the Clade I and Clade II variants is also discussed, with emphasis on the increased virulence and mortality related to Clade I and increased transmissibility of Clade II variants, including Clade IIb. Recent genomic studies have shown that hypermutations caused by the APOBEC3 enzymes, single-nucleotide polymorphism, and adaptive evolution contribute to viral persistence, immune escape, and epidemic spread. Furthermore, the review explains how epidemiologic surveillance efforts, molecular diagnostic tools, genomics techniques, and public health issues related to mpox epidemic response are managed. This information highlights the crucial role of genomics surveillance, timely diagnostics, vaccines, and the One Health approach in future prevention of mpox outbreaks.