Reproduction by binary fission generates a clonal genetic structure in bacterial populations in the absence of a high rate of recombination. The extent of recombination in natural populations of Neisseria gonorrhoeae was determined from an analysis of electrophoretically demonstrable allelic variation at structural genes encoding nine enzyme loci in 227 worldwide isolates. No significant linkage disequilibrium was evident in the population, indicating that recombination must be frequent, relative to binary fission. The genetic structure of N. gonorrhoeae was compared with that of Bacillus subtilis from an earlier study. Linkage disequilibrium was less extreme in the N. gonorrhoeae population than in the local population of B. subtilis, in which only modest clonal structure was evident. Thus, N. gonorrhoeae, unlike pathogens so far examined, has a non-clonal population structure. As expected in a freely recombining population, no correlation was found between electrophoretic genotype and serovar or auxotype.