The PorB porins are the major pore-forming proteins in the genusNeisseria. The trimeric PorB porins consist of 16 highly conserved transmembrane domains that form an amphipathic β-sheet connected by short periplasmic turns and eight extracellular hydrophilic loops. These loops are immunogenic and also play an important role in mediating antimicrobial influx. This study sought to (i) characterize the variations in Neisserial loop 3(355–438 bp) associated with intermediate resistance to penicillin/tetracycline and (ii) evaluate if there was evidence of horizontal gene transfer in any of the loops. We collated an integrated database consisting of 19 018Neisseriaspp. genomes – 17 882Neisseria gonorrhoeae, 114Neisseria meningitidisand 1022 commensalNeisseriaspp. To identify theporBalleles, a gene-by-gene approach (chewBBACA) was employed. To evaluate the presence of recombination events, the Recombination Detection Programme (RDP4) was used. In total, 3885porBalleles were detected. Paralogues were identified in 17Neisseriaisolates. Putative recombination was identified in loop regions. Intraspecies recombination amongN. gonorrhoeaeisolates and interspecies recombination betweenN. meningitidisand commensalNeisseriaspp., andN. gonorrhoeaeandN. lactamicawere identified. Here, we present a large-scale study of 19 018Neisseriaisolates to describe recombination and variation in the porB gene. Importantly, we found putative recombination in loop regions between the pathogenic and non-pathogenicNeisseriaspp. These findings suggest the need for pheno- and genotypic surveillance of antimicrobial susceptibility in commensalNeisseriaspp. to prevent the emergence of AMR in the pathogenicNeisseria. This article contains data hosted by Microreact.