Olive ridley (Lepidochelys olivacea) turtles migrate across tropical regions of the Atlantic, Pacific, and Indian Oceans. Worryingly, olive ridley populations have been declining substantially and is now considered a threatened species. In this regard, habitat degradation, anthropogenic pollution, and infectious diseases have been the most notorious threats for this species. We isolated a metallo-β-lactamase (NDM-1)-producingCitrobacter portucalensisfrom the blood sample of an infected migratory olive ridley turtle found stranded sick in the coast of Brazil. Genomic analysis ofC. portucalensisconfirmed a novel sequence type (ST), named ST264, and a wide resistome to broad-spectrum antibiotics. The production of NDM-1 by the strain contributed to treatment failure and death of the animal. Phylogenomic relationship with environmental and human strains from African, European and Asian countries confirmed that critical priority clones ofC. portucalensisare spreading beyond hospital settings, representing an emerging ecological threat to marine ecosystems.