Plant pathogens have the capacity to manipulate the host immune system through the secretion of effectors. We identified 27 putative effector proteins encoded in the genome of the maize anthracnose pathogen Colletotrichum graminicola that are likely to target the host’s nucleus as they simultaneously contain sequence signatures for secretion and nuclear localization. We functionally characterized one protein identified as CgEP1. This protein is synthesized during the early stages of disease development and is necessary for anthracnose development in maize leaves, stems and roots. Genetic, molecular and biochemical studies confirmed that this effector targets the host’s nucleus, and defines a novel class of dsDNA-binding protein. We show that CgEP1 arose from a gene duplication in an ancestor of a lineage of monocot-infecting Colletotrichum spp. and has undergone an intense evolution process with evidence for episodes of positive selection. We detected CgEP1 homologs in several species of a grass infecting lineage of Colletotrichum spp. suggesting that its function may be conserved across a large number of anthracnose pathogens. Our results demonstrate that effectors targeted to the host nucleus may be key elements for disease development, and aid in the understanding of the genetic basis of anthracnose development in maize plants.