Bluetongue virus (
BTV
), transmitted by midges (Culicoides sp), is distributed worldwide and causes disease in ruminants. In particular,
BT
can be a debilitating disease in sheep causing serious trade and socio‐economic consequences at both local and global levels. Across Australia, a sentinel cattle herd surveillance program monitors the
BTV
activity. Prior to 2014,
BTV
‐1, ‐2, ‐3, ‐7, ‐9, ‐15, ‐16, ‐20, ‐21 and ‐23 had been isolated in Australia, but no bluetongue disease has occurred in a commercial Australian flock. We routinely use a combination of serology, virus isolation,
RT
‐
PCR
and next generation and conventional nucleotide sequencing technologies to detect and phylogenetically characterize incursions of novel
BTV
strains into Australia. Screening of Northern Territory virus isolates in 2015 revealed
BTV
‐5, a serotype new to Australia. We derived the complete genome of this isolate and determined its phylogenetic relationship with exotic
BTV
‐5 isolates. Gene segments 2, 6, 7 and 10 exhibited a close relationship with the South African prototype isolate
RSA
rrrr/5. This was the first Australian isolation of a Western topotype of segment 10. Serological surveillance data highlighted the antigenic cross‐reactivity between
BTV
‐5 and
BTV
‐9. Phylogenetic investigation of segments 2 and 6 of these serotypes confirmed their unconventional relationships within the
BTV
serogroup. Our results further highlighted a need for a revision of the current serologically based system for
BTV
strain differentiation and importantly, implied a potential for genome segments of pathogenic Western
BTV
strains to rapidly enter Southeast Asia. This emphasized a need for continued high‐level surveillance of vectors and viruses at strategic locations in the north of Australia The expansion of routine characterization and classification of
BTV
to a whole genome approach is recommended, to better monitor the presence and level of establishment of novel Western topotype segments within the Australian episystem.