The treatment of infections from the sexually transmitted pathogen Mycoplasma genitalium is hampered by the rapidly increasing resistance to the recommended first- (macrolides) and second-line antibiotics (quinolones). Thus, resistance-guided therapy (RGT) is key for its successful eradication but the efficiency of this approach can be influenced by re-infections and treatment failures. The typing of strains is helpful to distinguish between ongoing colonization, re-infection or the development of resistance. In the present study, mgpB and MG_309 types as well as mutations associated with macrolide, quinolone and tetracycline resistance of strains in M. genitalium-positive samples accumulated in the years 2019 and 2020 at a university hospital were analyzed. Fifty-eight positive first and sixteen positive follow-up samples from patients (96.6% male, 84.5% men who have sex with men, 74.1% HIV-positive) were included. Twenty-three mgpB types (seven new types), nine MG_309 types and thirty-four mgpB/MG_309 types were identified. The prevalence of mutations associated with macrolide, quinolone and tetracycline resistance was 56.9%, 10.3% and 6.8%, respectively. Despite the fact that many asymptomatic patients were not treated and tests of cure were impossible in different cases, the preliminary rate of successful eradication (93.3%) in this study is promising for the continuation of the RGT strategy.