Copyright © 2017 American Sexually Transmitted Diseases Association. Background Macrolide and fluoroquinolone resistance is alarmingly emerging in M. genitalium worldwide. This article provides the first estimates of the current prevalence of macrolide and fluoroquinolone resistance-mediating mutations in Barcelona, Spain, and identifies risk factors associated with the acquisition of these resistances. Methods The study was conducted retrospectively with specimens submitted between February 2013 and March 2014 to the microbiology department of the Vall d'Hebron Hospital, Barcelona, where M. genitalium was detected using nucleic acid amplification methods. DNA sequencing of 23S ribosomal RNA gene and parC was performed in the Statens Serum Institut, Copenhagen, to detect genotypic macrolide and fluoroquinolone resistance markers, respectively. Results Macrolide resistance-mediating mutations were detected in 35% (95% confidence interval, 24%-47%) of the M. genitalium-positive episodes, whereas 8% (95% confidence interval, 3%-17%) carried fluoroquinolone resistance mutations. Of them, three cases harbored multidrug resistance to both classes of antibiotics. Men who had sex with men (P = 0.002) and treatment with azithromycin within the previous 12 months (P = 0.006) were strongly associated with macrolide resistance. Conclusion The widespread appearance of resistances, also in Spain, makes imperative the implementation of combined diagnostic-resistance detection assays for M. genitalium to facilitate the optimization of antibiotic treatment in the management of nongonococcal urethritis and potentially reduce the transmission of resistances.