Dengue virus (DENV) and chikungunya virus (DENV) are arboviruses of major public health importance. Monitoring circulation of medically important mosquito-borne viruses in the Indo Pacific region allows countries to predict disease outbreaks and prepare mitigation and control strategies. We have monitored long-Term molecular epidemiology of DENV and CHIKV in Indonesia and Western Australia (WA), with febrile Western Australian travellers returning from Indonesia as sentinels. Our findings provide insights into the transmission dynamics of CHIKV genotypes and DENV serotypes, genotypes and lineages in the region and virus importation to WA. Our ongoing studies provide valuable and timely information on transmission of emerging and re-emerging arboviruses in the Indo Pacific region and furthermore provide detailed genomic data that inform our understanding of viral and epidemic virulence.