Reliable data concerning the incidence and phenotypic and genotypic characteristics of the Neisseria gonorrhoeae population in many eastern European countries are lacking. Clinically significant N. gonorrhoeae isolates (n = 76) from 76 consecutive patients in Arkhangelsk, Russia were characterised by antimicrobial susceptibility testing, serovar determination, porB gene sequencing and N. gonorrhoeae multi-antigen sequence typing (NG-MAST). The isolates were assigned to 12 different serovars, displayed 35 divergent porB sequences, and belonged to 40 different sequence types (STs). All the serovars, but only seven of the STs, had been identified previously in other countries. Twelve ST clusters of between two and 14 isolates were identified, which indicated that many multiple transmission networks exist in Arkhangelsk. The high number of unique STs (n = 28) may be a consequence of sub-optimal diagnostic procedures, ineffective partner tracing, local emergence of new STs, import of strains via sexual tourists, or foreign travel. The N. gonorrhoeae population circulating in Arkhangelsk was highly diverse and differed from the N. gonorrhoeae populations disseminated in some western European countries. Thorough knowledge concerning the incidence of gonorrhoea, antibiotic susceptibility and other phenotypic and genotypic characteristics of the N. gonorrhoeae strains circulating in eastern Europe is crucial.