Complete Type VI Secretion Systems were identified in the genome sequence data ofNeisseria subflavaisolates sourced from throat swabs of human volunteers. The previous report was the first to describe two complete Type VI Secretion Systems in these isolates, both of which were distinct in terms of their gene organization and sequence homology. Since publication of the first report, Type VI Secretion System subtypes have been identified inNeisseriaspp. The characteristics of each type inN. subflavaare further investigated here and in the context of the otherNeisseriaspp., including identification of the lineages containing the different types and subtypes. Type VI Secretion Systems use VgrG for delivery of toxin effector proteins; several copies ofvgrGand associated effector / immunity pairs are present inNeisseriaspp. Based on sequence similarity between strains and species, these core Type VI Secretion System genes,vgrG, and effector / immunity genes may diversify via horizontal gene transfer, an instrument for gene acquisition and repair inNeisseriaspp.