Arboviral infections are a significant threat to the health of Australian Defence Force (ADF) personnel with the potential to reduce operational capability. In March 2016, 28 of 128 personnel from a single unit had laboratory confirmed Ross River virus (RRV) infections following a military training exercise in the Shoalwater Bay Training Area (SWBTA) in central Queensland. In May 2017, 34 ADF personnel presented with symptoms of epidemic polyarthritis while on a military training exercise in same area. In both outbreaks, the location of the patients and the timing of the onset of symptoms suggested person-mosquito-person transmission of virus. As part of the outbreak investigation, consent was obtained to attempt viral isolation from 7 serum samples from the 2016 outbreak and 10 serum samples from the 2017 outbreak. RRV was isolated from one 2017 sample and one 2016 sample. Phylogenetic analysis of envelope gene 2 (E2) and non-structural protein 3 (nsP3) genes revealed that these two viruses belonged to two different lineages. The 2016 ADF isolate most closely resembled a strain of RRV recovered in Queensland in 2004 (QML1) (99.3% nucleotide and amino acid identity) while the 2017 ADF isolate most closely resembled strains of RRV isolated in Queensland more recently (2015) (99.8% nucleotide and 99.3% amino acid identity). Direct comparison of the E2 protein of both RRVs revealed there is one N-glycosylation site and 6 amino acid changes located at A and C domains of E2, which are important for interaction with the E1 protein. The nsP3 genes of both the RRVs contained the repeated 12 amino acid sequence element characteristic of post-1979 strains of RRVs. These results indicate that two different RRVs caused the 2016 and 2017 ADF SWBTA outbreaks. The re-emergence of the QML1 lineage may pose a problem for the ADF and for public health in Australia.