Piscine lactococciosis is a significant threat to both cultured and wild fish populations, causing high morbidity and mortality. Historically, the disease was attributed to *Lactococcus garvieae*, but recent studies have identified three distinct species—*L. garvieae*, *L. petauri*, and *L. formosensis*—that cause lactococciosis. These species are phenotypically and genetically similar, leading to widespread misidentification. This study aims to update our understanding of lactococciosis and improve identification methods. Using representative isolates from each species, the authors compared various molecular and phenotypic typing assays, including whole-genome sequencing (WGS), PCR assays, MALDI-TOF MS, biochemical tests, and antimicrobial profiling. WGS and *gyrB* gene sequencing were the most accurate methods for species identification. A qPCR assay based on a putative glycosyltransferase gene also distinguished *L. petauri* from *L. garvieae/formosensis*. Biochemical tests and MALDI-TOF MS showed some species-specific patterns but required additional analyses. The three species demonstrated overlapping host and geographic ranges but differed in host specificity, regional prevalence, and antimicrobial susceptibility. *L. petauri* is particularly problematic in trout facilities and may carry tetracycline resistance genes. Accurate and practical diagnostic methods are crucial for disease management, and the study recommends whole-genome or *gyrB* sequencing for species identification and a qPCR assay or a sucrose test for specific identification of *L. petauri*. Understanding the local diversity of lactococcal species will enable better resource allocation, biosecurity measures, vaccination, and treatment interventions to limit disease spread and economic losses.Piscine lactococciosis is a significant threat to both cultured and wild fish populations, causing high morbidity and mortality. Historically, the disease was attributed to *Lactococcus garvieae*, but recent studies have identified three distinct species—*L. garvieae*, *L. petauri*, and *L. formosensis*—that cause lactococciosis. These species are phenotypically and genetically similar, leading to widespread misidentification. This study aims to update our understanding of lactococciosis and improve identification methods. Using representative isolates from each species, the authors compared various molecular and phenotypic typing assays, including whole-genome sequencing (WGS), PCR assays, MALDI-TOF MS, biochemical tests, and antimicrobial profiling. WGS and *gyrB* gene sequencing were the most accurate methods for species identification. A qPCR assay based on a putative glycosyltransferase gene also distinguished *L. petauri* from *L. garvieae/formosensis*. Biochemical tests and MALDI-TOF MS showed some species-specific patterns but required additional analyses. The three species demonstrated overlapping host and geographic ranges but differed in host specificity, regional prevalence, and antimicrobial susceptibility. *L. petauri* is particularly problematic in trout facilities and may carry tetracycline resistance genes. Accurate and practical diagnostic methods are crucial for disease management, and the study recommends whole-genome or *gyrB* sequencing for species identification and a qPCR assay or a sucrose test for specific identification of *L. petauri*. Understanding the local diversity of lactococcal species will enable better resource allocation, biosecurity measures, vaccination, and treatment interventions to limit disease spread and economic losses.