Yaws is an endemic disease caused by Treponema pallidum subsp. pertenue (TPE) that primarily affects children in rural regions of the tropics. • Clinical manifestations in the primary stage include chronic skin ulcers and other skin lesions, potentially affecting bones and cartilage in the later stages. • A newly developed multilocus sequence typing (MLST) scheme for TPE isolates was used to characterize the bacterium causing yaws in the Namatanai District, New Ireland province of Papua New Guinea during the Yaws 3 Trial. • This multi-locus sequence typing (MLST) scheme was applied to TPE-containing clinical isolates obtained during a mass drug administration study conducted in the Namatanai District of Papua New Guinea between June 2018 and December 2019 (John et al. 2022). • Out of the 1081 samples collected, 302 (28.5%) tested positive for TPE DNA, and 255 (84.4%) of these samples were fully typed.