Mycoplasma genitalium is a sexually transmitted urogenital pathogen, and infection can result in serious symptoms. As M. genitalium is rather difficult to culture, infections are usually detected by molecular methods. Unfortunately, there has recently been a significant increase in resistance to azithromycin and moxifloxacin used for the treatment of M. genitalium infections. The increased resistance to (often empirically prescribed) M. genitalium treatments has resulted in frequent therapy failure, and stresses the need for routine detection of antibiotic resistance. In M. genitalium, antibiotic resistance is almost always the result of DNA mutations and thus can easily be detected by molecular techniques. Regrettably, many microbiology laboratories do not use molecular techniques for the detection of bacterial antibiotic resistance. As molecular tests are becoming available for M. genitalium, both for the establishment of infections and detection of antibiotic resistance, it is now more important to ensure that the knowledge on the resistance mechanisms is transferred from the laboratory to the clinician. This review will provide a brief summary of the current status of antibiotic resistance, their molecular mechanisms, and the impact on the current status of M. genitalium treatment.