Fundação Oswaldo Cruz, Salvador, Brazil (T. Gräf, J.G. de Jesus); Fundação Oswaldo Cruz, Rio de Janeiro, Brazil (C. Vazquez, M. Giovanetti, F. de Bruycker-Nogueira, V. Fonseca, J. Xavier, M.C.L. de Mendonça, A.M. Bispo de Filippis, L.C.J. Alcantara); Laboratorio Central de Salud Pública, Asunción, Paraguay (C. Vazquez, A. Gómez, S. Villalba, J. Torales, M.L. Gamarra); Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil (M. Giovanetti, V. Fonseca, J. Xavier, V. Azevedo, L.C.J. Alcantara); University of KwaZulu-Natal, Durban, South Africa (V. Fonseca, T. de Oliveira); Universidade de São Paulo, São Paulo, Brazil (I.M. Claro); University of Oxford, Oxford, UK (J. Thézé); University of Washington, Seattle, Washington, USA (T. de Oliveira); Organización Panamericana de la Salud /Organización Mundial de la Salud, Panama City, Panama (L. Franco); Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília, Brazil (C.F. Campelo de Albuquerque); Dirección General de Vigilancia de la Salud Paraguay, Asunción (S. Irala); The University of Sydney, Sydney, New South Wales, Australia E.C. Holmes); Pan American Health Organization/World Health Organization, Washington, DC, USA (J.A.M. Rico)Decit/SCTIE/MoH and CNPq (440685/2016-8 and 440856/2016-7); by CAPES (88887.130716/2016-00, 88881.130825/2016-00, and 88887.130823/2016-00), and by the EU Horizon 2020 Programme through ZIKAlliance (PRES-005-FEX- 17-4-2-33). M.G. is supported by the Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro–FAPERJ. E.C.H. is supported by an Australian Research Council Australian Laureate Fellowship (FL170100022). A.M.B.F. was supported by International Development Research Centre, Canada (grant 108411-001) and by Horizon 2020 through ZikaPlan and ZikAction (grant agreement nos. 734584 and 734857).Paraguay has been severely aff ected by emergent Zika and chikungunya viruses, and dengue virus is endemic. To learn more about the origins of genetic diversity and epidemiologic history of these viruses in Paraguay, we deployed portable sequencing technologies to strengthen genomic surveillance and determine the evolutionary and epidemic history of arthropod-borne viruses (arboviruses). Samples stored at the Paraguay National Central Laboratory were sequenced and subjected to phylogenetic analysis. Among 33 virus genomes generated, we identifi ed 2 genotypes of chikungunya and 2 serotypes of dengue virus that circulated in Paraguay during 2014– 2018; the main source of these virus lineages was estimated to be Brazil. The evolutionary history inferred by our analyses precisely matched the available travel history of the patients. The genomic surveillance approach used was valuable for describing the epidemiologic history of arboviruses and can be used to determine the origins and evolution of future arbovirus outbreaks.