Since the formation of a committee under the guidance of R. E. Buchanan in 1936, microbiologists have developed and refined a nomenclatural code for bacteriology, the International Code of Nomenclature of Prokaryotes (ICNP). This code has greatly facilitated recent advances in taxonomy and related fields of microbiology. Technical developments in omics have led to a surge in genome-based discoveries of novel uncultured species, many of which play important roles in environmental and medical microbiology. Nevertheless, the ICNP only recognizes cultures as nomenclatural types, thereby preventing the names of the uncultured microorganisms from being validly published. To compensate for the ineffectiveness of the ICNP in creating permanent and stable names of uncultured taxa, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode) was published in 2022. The SeqCode was formed with the intention of complementing and someday merging with the ICNP. However, as the two nomenclatural codes currently work independently, the consequences of the concurrence of both codes on the scientific community are still not clear. Here, we introduce the histories and principles of the ICNP and SeqCode, summarize their advantages and limitations, and call for scholars to both respect and utilize the two nomenclatural codes of prokaryotes, aiming to facilitate the establishment of a more reasonable and beneficial naming system.