The genus Flavobacterium comprises approximately 300 species that inhabit a wide variety of habitats, including soil, ice, freshwater, and marine life. Due to advances in genomic sequencing studies, new proposals have been developed and adopted by the International Committee on Prokaryotic Nomenclature for species delineation based on genomic indices. The main indices are average nucleotide identity (ANI), which is the similarity of loci shared between two genomes; digital DNA-DNA hybridization, which determines the percentage of homologous loci between two genomes; and GC content, which represents an important source of evolutionary information for comparison between species. Among the species of the genus, important pathogens for inland fish farming stand out, and new species have been atypically identified in fish around the world in recent years. Because species of the genus are readily found in aquatic ecosystems, the pathogenic potential of species not commonly associated with clinical cases in fish should be monitored. Strain Df2 isolated from kidney of Piaractus mesopotamicus was molecularly identified as F. inkyongense (PP409973.1) according to 16S rRNA similarity with the type strain database (99.8% similarity to the F. inkyongense type strain IMCC27201). Further analysis using the NCBI nucleotide collection and reference genomes databases indicated the same similarity to F. johnsoniae subsp. aurantiacum (syn. Flexibacter aurantiacum subsp. excathedrus), previously isolated from fish in Thailand and from diseased chocolate cichlids (Hypselecara coryphaenoides) in the United States, where F. inkyongense was identified as the infectious agent. The absence of a complete genome for F. inkyongense complicates precise taxonomic delineation, underscoring the need for genomic resolution to clarify the relationship between these two taxa. So, for this purpose genomic sequence was carried out to compare genomic overhall related indices against genomes deposited under the NCBI database. As a result, no similarity was found using software fastANI nor DNA-DNA hybridization, supporting the evidence that F. inkyongense is a unique species with Flavobacterium johnsoniae subesp excathedrus isolates from fish being the same species. The best similarity was observed with Costa-Rica 04-02-TN (NZ_CP067377.1), 79,45% (ANI) with 30,9% aligned region; these values certainly were out threshold proposed by species delineation. Further studies will involve obtaining data from genomic annotations and experimental challenges to understand the virulence mechanisms of this species in fish. We hope our results contribute to the taxonomy of the Flavobacterium genus as an improvement for the monitoring of emerging fish diseases caused by this bacteria genus in fish.