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Neisseria meningitidis (Nm) and N. gonorrhoeae (Ng) are closely related pathogenic bacteria. Using those genes found across 20 Nm and 15 Ng genomes we find that Nm is 7x more diverse than Ng in their combined core genome. Both species have acquired the majority of their diversity by recombination with divergent strains, however we find that Nm has acquired more of its diversity by recombination than Ng. We find that linkage disequilibrium declines rapidly across both species. Several observations suggest that Nm has a higher effective population size than Ng; it is more diverse, the ratio of non-synonymous to synonymous polymorphism is lower, and LD declines more rapidly to a lower asymptote. The two species share a modest amount of variation, half of which seems to have been acquired by lateral gene transfer and half from their common ancestor. We investigate whether diversity varies across the genome of each species and find that it does. Much of this variation is due to different levels of lateral gene transfer. However, we also find some evidence that the effective population size varies across the genome. We test for adaptive evolution in the core genome and found some evidence.