Dengue virus (DENV) infection continues to be one of the greatest health burdens for Australian Defence Force (ADF) personnel conducting operations in East Timor (ET). In this study 72 DENV E-genes, including 15 DENV1, 37DENV2, 9 DENV3 and 11 DENV4, were sequenced from 323 samples collected from ADF members presenting with febrile symptoms whilst deployed to ET at the outset of Australia’s Defence Cooperation Program (period 2001 – 2002) as well as samples collected over the period Dec 2009 – Mar 2012. Phylogenetic tree analysis revealed the presence of all four DENV serotypes with multiple viral lineages co-circulating within affected ADF members. All ADF DENV1, DENV3 and DENV4 were classified as a homologous genotype (genotype I, genotype I and genotype II, respectively) while DENV2 was classified as cosmopolitan genotype. The majority of these strains were closely related to lineages known to have circulated in separate SE Asian countries which indicate multiple introductions DENV into Timor Island. It is speculated that this may to some degree be a direct result of pathogen importation through the multinational involvement of UN personnel over successive deployments to support peace-keeping operations in the youngest nation in the region. In addition a recombinant DENV2 and a recombinant DENV3 virus were identified. Direct comparison of ET DENV3 2012 ADF isolates with reported ET DENV 2005 isolates revealing three important amino acid mutations in the envelope gene, namely, 124AA Serine to Leuine, 140AA Isoleucine to Serine and 459AA Valine to Alanine. The 124AA and 140AA sites are located within Domain II and Domain I of the E-Protein which are the epitope domains for neutralizing antibodies. 459AA is found at TMD1 which is critical for virus assembly and secretion. These significant conformational alterations of the E-Protein warrant further investigation to determine whether these mutations improve DENV viral fitness.