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Microorganisms responsible for genitourinary infections increasingly include species other than conventional etiological agents that are of clinical and pathogenic relevance and therapeutic interest. This cross-sectional descriptive study selected samples from clinical genitourinary episodes between January 2016 and December 2019 in which emerging microbiological agents were detected. The patients’ epidemiological characteristics, clinical presentation, antibiotic treatment, and outcome were studied to identify their pathogenic role. The emerging microorganisms most frequently detected in urinary tract infections were <i>Streptococcus bovis</i> (58.5%) and <i>Gardnerella</i> spp. (23.6%) in females and <i>S. bovis</i> (32.3%), <i>Aerococcus urinae</i> (18.6%), and <i>Corynebacterium</i> spp. (16.9%) in males, while the most frequently detected in genital infections were <i>S. viridans</i> (36.4%) in females and <i>C. glucuronolyticum</i> (32.2%) and <i>Gardnerella</i> spp. (35.6%) in males. All cases in female children were produced by <i>S. bovis.</i> Symptomatic episodes were more frequent with <i>Aerococcus</i> spp. and <i>S. bovis</i> and the presence of leukocytosis more frequent with <i>Aerococcus</i> spp. Quinolones and doxycycline were most often prescribed antibiotics for genital infections and quinolones and amoxicillin-clavulanic acid for urinary infections. Urinary infection by <i>Aerococcus</i> spp. was more frequent in males of advanced age, <i>Corynebacterium</i> spp. was more frequent in permanent vesical catheter carriers, and episodes of asymptomatic bacteriuria by <i>Gardnerella</i> spp. were more frequent in patients with kidney transplant and chronic consumers of corticosteroid therapy. <i>Lactobacillus</i> spp. should be considered in urinary infections of patients of advanced age and with a previous antibiotic load. Genital infection by <i>Gardnerella</i> spp. was significantly associated with a history of risky sexual relations.