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Abstract Background Gordonia polyisoprenivorans is a ubiquitous aerobic actinomycetes bacterium that rarely cause infections in humans. Here, we report a case of G. polyisoprenivorans catheter-related bacteremia in an AIDS patient. Case presentation A 37-year-old man with a past medical history of AIDS-related lymphoma suffered bacteremia caused by a Gram-positive corynebacterium. The strain was identified as a Gordonia species by matrix-assisted laser desorption ionization–time of flight mass spectrometry and confirmed to G. polyisoprenivorans by 16S rRNA combined with gyrB gene sequencing analyses. The patient was treated with imipenem and had a good outcome. Conclusions The findings from our case and previously reported cases indicate that malignant hematologic disease, immunosuppression, and indwelling catheter heighten the risk for G. polyisoprenivorans infection. Molecular methods should be employed for proper identification of G. polyisoprenivorans to the species level.