The appearance for viruses that evolve to adapt to a new living niche often reflect on viral sequence changes. Fixation of these changes may require a long time through repeated transmission, thereby rendering a reduced size of an effective population harboring dominant alterations in their sequence spaces. Those approaches, with which we can closely monitor and survey the transient changes of viral sequences over the longer timescales, thus become a requisite to better understand the evolution of viral pathogenicity. Molecular barcodes are a powerful and practical molecular tool to individually label sequences, allowing for correcting sequencing errors and identifying true mutants of interest with a single nucleotide resolution. Molecular barcoding has also been implemented as a useful approach to study several zoonotic viruses. In this review, the emphasis will not only be limited to summarize current studies focusing on viral pathogenesis and fitness; we will also propose ideas that molecular barcodes can be used to execute surveillance of changes of viral sequences. We believe that this review will be helpful for the readers to better understand the rationale and the usage of molecular barcodes and the perspectives of what molecular barcodes can do for fighting upcoming emerging infectious diseases.