Recombinant plasmids harbouring the functional M.NgoPII methyltransferase (specificity 5'-GGCC-3') were isolated from amplified gene libraries of gonococcal chromosomal DNA cloned in pBR322 and in Escherichia coli RR1. The M.NgoPII gene was localized by sub-cloning and the nucleotide sequence of a cloned 1.6 kb segment of Neisseria gonorrhoeae DNA harbouring the methylase gene was determined. This data, coupled with sub-cloning experiments and in vitro transcription-translation studies, indicates a theoretical size of 38.5 kd for the methylase protein. The predicted amino acid sequence of the methylase contains significant regions of homology with the projected sequences of other cytosine-modifying methylases, upon which the activity of these enzymes is likely to depend.