Ongoing emergence and spread of Neisseria gonorrhoeae antimicrobial resistance (NG-AMR) is of global concern and was recently prioritised as an “urgent threat” (the highest threat level) by the United States Centers for Disease Control and Prevention. The Gonorrhoea Resistance Assessment by Nucleic Acid Detection (GRAND) study is an NHMRC-funded study that began in 2012. The key aims of this study are to (a) assess the genetic mechanisms that underpin NG-AMR with a view to developing molecular NG-AMR detection methods and (b) better understand the spread of gonococcal infection in Australia. To initially address these aims, we genotyped all available N. gonorrhoeae isolates collected in Australia in the first six months of 2012 (n = 2228) using a novel single nucleotide polymorphism (SNP)-based typing method targeting informative SNPs on gonococcal house-keeping and resistance genes. Preliminary analysis has identified 294 distinct gonococcal strains in Australia in the 6-month study period. The majority of isolates were dominated by a relatively small number of strains; the 40 most prevalent strains accounted for more than 80% of all gonococci, and of these, the top three most prevalent strains comprised approximately 25% of all isolates. Using a male to female ratio we are also able to assign strains to men who have sex with men (MSM) or heterosexual networks. Of the top three prevalent strains, two were predominantly found in heterosexuals and one in MSM. The GRAND study data also show the appearance of numerous unique genotypes in our population, with 55% of strains represented by only one isolate. Temporal variation in strain prevalence based on two-monthly time periods was also evident. Overall these molecular data show considerable genotypic diversity of gonococcal strains in the Australian population, and highlight the ability of certain gonococcal strains to become established in sexual networks.