Neisseria gonorrhoeae is an obligate human pathogen causing gonorrhea the second most reported bacterial sexually transmitted infection. High level genomic plasticity of this pathogen requires whole genome sequence (WGS) analysis for epidemiological investigations. The absence of N. gonorrhoeae genomic data from Bangladesh represents a critical gap in South Asian gonococcal genomic epidemiology. Here we report a genomic investigation of N. gonorrhoeae from Bangladesh using WGS approach.