Infectious diseases are not only a threat to humans and animals but also to an entire ecosystem if the three axis of One Health are considered. Elizabethkingia miricola is a water-borne and opportunistic pathogen frequently evolving to high morbidity and mortality outcomes. More recently, reports on E. miricola infections causing death in different anuran species are increasing. Here, we reported the emergence, in a clinical setting in Brazil (Amazon region), of an E. miricola (EM15) with an almost untreatable antibiotic resistance phenotype that was closely related to the lineage involved with anuran infections worldwide. A genomic reconstruction revealed that EM15 belonged to a cluster represented by genomes from human and animal (anurans) sources recovered from China, Europe, and the Americas from 2002 to 2021, and from the Space Station Mir condensation water. Their resistome and virulome were also in agreement with their genetic relationship since they harboured the same set of resistance and putative virulence genes. Therefore, the emergence of EM15 in a clinical setting in the Amazon region, a hotspot area of anuran diversity and home to Amerindian groups that live in close relationship with the wildlife, may represent a warning to the public and environmental health.