Background: The prevalence of sexually transmitted infections (STIs) is high in New Caledonia (NC), but there are no data on Mycoplasma genitalium (MG). However, the syndromic treatment of urethritis used in the territory includes a single dose of azithromycin, which could generate resistance in MG. Methods: We recruited 217 men referred to the Noumea public medical centre (CMP) with signs of urethritis and meeting the inclusion criteria from May 2016 to March 2018. Each was tested for Neisseria gonorrhoeae (NG), Chlamydia trachomatis (CT), Trichomonas vaginalis (TV) and for the first time in NC for MG by polymerase chain reaction (PCR). Results: The prevalence of MG was 10.1% (22/217). Azithromycin resistance of MG (mutation in the 23S rRNA gene) could only be assessed for 10 of the 22 strains. Only one (1/10; 10%) was resistant. The prevalence of other STIs tested was high, as CT, NG and/or TV were associated in 77.3% (17/22) of MG-positive cases. Conclusions: Although co-infections further justify syndromic management, the presence of MG in NC urethritis cases could call treatment guidelines into question.