Epidemic polyarthritis (EPA) caused by Barmah Forest virus (BFV) infection is the second most frequently notified arboviral diseases after Ross River virus (RRV) in Australia with approximately 1,200 cases reported annually over the last decade. The prototype strain of BFV (BH2193) was isolated from Cx. annulirostris trapped near the Barmah Forest area of Northern Victoria in 1974. Since then, outbreaks have been recorded in every Australian state as well as Papua New Guinea. Two BFV strains were isolated from Australian Defence Force (ADF) training areas (TA). MIDITully.2017 strain was isolated from a homogenized pool of Verrallina spp. mosquitoes captured in ADF Tully TA (17.9° S, 145.9° E), Queensland 2017 while MIDIWB78.2018 strain was isolated from a homogenized pool of Cx. annulirostris mosquitoes captured in ADF Wide Bay TA (25.3° S, 152.8° E), Queensland in 2018. The complete nucleotide sequences comparison with the only available whole genome sequence in GenBank, the prototype BFV BH2193 strain, revealed remarkable conservation between 1974 and 2018 with a maximum divergence of only 2.7% genome wide, but both ADF BFV strains contain multiple nucleotide insertions in the 3’ untranslated region (UTR). At the amino acid level, MIDITully.2017 and MIDIWB78.2018 have a total of 32 and 33 amino acid substitutions evenly spread in non-structural and structural proteins, respectively. These mutations/deviations from the prototypic sequence and the insertions in the 3’UTR might have a dramatic impact on viral fitness and disease transmission capacity of the virus warranting further investigation. Phylogenetic analysis of all available BFV E2 nucleotide sequences deposited in GenBank between 1974 and 2019 segregated the viruses obtained by ADF into one of two BFV clades.