Methylobacterium populi is a fastidious, pink-pigmented, Gram-negative bacterium that has been isolated from poplar trees that are found throughout the Northern Hemisphere in both temperate and subtropical regions. Herein, we report a novel case of M. populi peritonitis associated with continuous ambulatory peritoneal dialysis (CAPD). A 45-year-old Japanese man with a history of hypertension and chronic kidney disease was diagnosed with CAPD-associated peritonitis. After starting broad-spectrum antibiotics, white blood cell (WBC) count in the CAPD effluent remained elevated. On day 7, the CAPD effluent grew Gram-negative vacuolated rods identified as M. populi using 16S ribosomal RNA gene sequences. After the treatment regimen was changed to intraperitoneal gentamicin, the WBC count in the CAPD effluent decreased, and the clinical features improved. Although infection with M. populi is rare, clinicians should advise patients on CAPD to avoid contact with poplar trees and provide training on adherence to CAPD exchange protocols, including hand hygiene.