Painful granulomatous lesions appeared on the face of a 36-year-old man with myelodysplastic syndrome. Skin biopsy revealed chronic inflammatory granuloma. Bacterial cultures of the lesions and blood indicated the same unknown Gram-negative rod bacterium. The 16S ribosomal RNA sequence of the unknown bacterium yielded Phenylobacterium. Thus, we diagnosed cutaneous infectious granuloma caused by Phenylobacterium and myelodysplastic syndrome/refractory cytopenia with multi-lineage dysplasia. After treatment with combined antibacterials that were selected based on the tests for drug sensitivity, the lesions disappeared with only scars remaining and without any signs of relapse after 1 year. This is the first case report of cutaneous infectious granuloma caused by Phenylobacterium.