© Boan et al. Background: PorA, fetA and fHbp are three antigen encoding genes useful for meningococcal typing and FHbp is an important component of meningococcal B vaccines. Methods: We performed sequence analysis of meningococcal , and genes on 128 isolates from Western Australia, relating results to age, gender, race and geographic region. Results: We found predominantly PorA subtypes P1.22,14-16 (n=23) and P1.7-2,4 (n=19); FetA subtypes F1-5 (n=41), F3-6 (n=11), F5-1 (n=10), F5-2 (n=9), F5-5 (n=8), F3-3 (n=8); and FHbp variant groups 1 (n=65) and 2 (n=44). PorA P1.22,14-16 and FHbp variant group 2 were associated with younger age and aboriginality. Conclusions: FHbp modular groups of the bivalent recombinant FHbp vaccine and the multicomponent 4CMenB vaccine make up 8.3% and 47.7% respectively of the examined serogroup B isolates from 2000-2011, however to estimate vaccine efficacy requires an account of all vaccine antigens and their levels of expression.