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The detection of emerging pathogens responsible for genitourinary infections has increased with technological advances. We conducted a systematic review of publications on the involvement of these microorganisms in genitourinary samples, and we also investigated their presence and antibiotic susceptibility in samples from patients at our regional hospital (Granada, Spain). The MEDLINE database was searched up to 31 December 2020, and a cross-sectional descriptive study was performed of results obtained in urine samples and genital exudates from January 2016 through December 2019. The review highlighted the frequent involvement of Neisseria meningitidis in genital infections, while the data on other microorganisms were consistent with findings in our patient series. The emerging microorganisms most often responsible for urinary tract infections were Streptococcus bovis (58.5%) and Gardnerella vaginalis (23.6%) in females, and S. bovis (32.3%), Aerococcus urinae (18.6%), and Corynebacterium spp. (16.9%) in males; those most frequently reported in genital infections were S. viridans (36.4%) in females and C. glucuronolyticum (32.2%) and G. vaginalis (35.6%) in males. In general, emerging pathogens are resistant to conventional antibiotics such as penicillin. However, there has also been an increase in beta-lactam resistance by the S. bovis group and Corynebacterium spp. The systematic review showed that emerging microorganisms are responsible for only a small percentage of genitourinary infections but are of major clinical interest, with a predominance of the S. bovis group, G. vaginalis, Lactobacillus spp., Aerococcus spp., and Corynebacterium spp. in urine samples and of G. vaginalis and C. glucuronolyticum in genital samples. Given the increasing resistance to antibiotics empirically prescribed in patients with genitourinary infections, it is recommended to create an antibiogram in all cases.