Streptococcus agalactiae, commonly known as Group B Streptococcus (GBS), is a major neonatal pathogen. Due to this, pregnant women are screened by risk- or culture-based methods, resulting in intrapartum antibiotic administration to those identified as positive by screening. Culture-based methods for GBS detection provide minimal data regarding the prevalent serotypes of GBS and generate no data on other potential therapeutic targets. Whole genome sequencing (WGS), however, generates detailed information about circulating strains and population dynamics. We generated WGS data on 141 antenatal vaginal and rectal GBS isolates and 10 neonatal disease GBS isolates from Western Australia using the Illumina NextSeq. Multi-locus sequence analysis revealed the presence of 28 previously described sequence types (ST) and one new ST. Phylogenetic analysis revealed general clustering based on serotype, and neonatal disease isolates to be dispersed amongst the antenatal colonising isolates. Of the clinical isolates sequenced, the most prevalent serotypes were Ia (25.5%), III (23.2%) and V (20.5%), followed by II (14.6%), Ib (6%), VI (5.3%), IV (4%) and VIII (0.7%). Examination of surface protein genes revealed no rib or bca genes present, while fibrinogen-binding protein, laminin-binding protein and serine peptidase genes were present in 99% and alp2 and alp3 genes in 3% of isolates. WGS allowed the identification of gene targets that are of particular importance for estimating candidate vaccine coverage. Current vaccines targeting the capsule are in development, with a trivalent (Ia, Ib and III) vaccine in clinical trials, however, as evident from the range of serotypes present and prevalence of serotype V this may only be effective for a proportion of the population. The genes encoding surface proteins for laminin- and fibrinogen-binding, and serine peptidases, were present in the majority of the GBS genomes analysed and may be promising candidate targets if expressed. Our data suggest that, for Western Australia, current GBS vaccines in development may not provide adequate protection based on the circulating serotypes observed.