Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)We present polymorphic microsatellite markers isolated for genetic studies of the sugarcane borer, Diatraea saccharalis (Fabricius). We isolated 16 microsatellite loci through an enriched genomic library protocol. After characterization, 12 markers showed polymorphic information expressed in the observed number of alleles (ranging from 2 to 7; 5 on average) and in the polymorphism information content (ranging from 0.292 to 0.771; 0.535 on average). These markers can be used in further studies to understand the basic ecological characteristics of the sugarcane borer, e.g., dispersion patterns and population genetic differentiation, associated with distinct geographic scales and host plants.12216311635Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)CNPq [578509/2008-3, 480619/2008-5, 484338/2011-0]CAPES [0103/08-0]