Antimicrobial resistance in Neisseria gonorrhoeae (NG) represents a global public health threat. NG has progressively developed resistance to current and previously recommended antibiotics, including the currently recommended treatment, ceftriaxone. Pharyngeal NG infections can contribute to the sustained transmission of gonorrhea as pharyngeal infections are often asymptomatic, can persists, and remain undiagnosed. Pharyngeal NG infections play a major role in the emergence of antimicrobial resistance in NG as horizontal gene transfer of resistance markers is common between NG and commensal Neisseria species which colonize the oropharynx. We review the evidence on the contribution of pharyngeal NG infections and commensal Neisseria species to the emergence of antimicrobial resistance in NG, outline research gaps, and propose potential research topics. Improved understanding of pharyngeal NG pathogenesis and how NG acquires antimicrobial resistance markers through horizontal gene transfer from commensal Neisseria species is critical to curtail the rapid evolution of antimicrobial resistance in NG and preserve the clinical utility of currently available and future antimicrobials.