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The majority of serogroup B isolates belonged to ST-41\/44 (41\u200a%) and ST-32 complex (16\u200a%). Comparing the time periods, before and after the decline of serogroup B invasive disease, there was a decrease of ST-41\/44 complex sequences (<jats:italic>P<\/jats:italic>=0.002). We observed the expansion of a sub-lineage within ST-41\/44 complex sequences being associated with isolation from the 1979\u20132003 time period (<jats:italic>P<\/jats:italic>=0.014). Isolates belonging to this sub-lineage expansion within ST-41\/44 complex were marked by four antigen allele variants. Presence of these allele variants was associated with isolation from the 1979\u20132003 time period after correction for multiple testing (Wald test, <jats:italic>P<\/jats:italic>=0.0043 for FetA 1\u20135; <jats:italic>P<\/jats:italic>=0.0035 for FHbp 14; <jats:italic>P<\/jats:italic>=0.012 for PorA 7\u20132.4 and <jats:italic>P<\/jats:italic>=0.0031 for NHBA two peptide allele). These sequences were associated with 4CMenB vaccine coverage (Fisher\u2019s exact test, <jats:italic>P<\/jats:italic>&lt;0.001). Outside of the sub-lineage expansion, isolates with markedly lower levels of predicted vaccine coverage clustered in phylogenetic groups showing a trend towards isolation in the 2006\u20132013 time period (<jats:italic>P<\/jats:italic>=0.08). In conclusion, we show the emergence and decline of a sub-lineage expansion within ST-41\/44 complex isolates concurrent with a hyperendemic period in meningococcal meningitis. The expansion was marked by specific antigen peptide allele combinations. 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