Vacuolar Myelinopathy (VM) is a neurological disease caused by exposure to aetokthonotoxin (AETX), a neurotoxin produced by the cyanobacteria Aetokthonos hydrillicola growing epiphytically on Hydrilla verticillata. Vacuolar Myelinopathy causes mortality in bald eagles and other wildlife in the Southeastern US by inducing vacuoles in white brain matter. Field molecular detection protocols allow for the detection of the cyanobacterium with minimal time and equipment. In this study, we developed a LAMP (Loop-Mediated Isothermal Amplification) protocol for the molecular detection of A. hydrillicola in a field setting. The primer set targets the toxin gene cluster associated with the production of AETX, which ensures high specificity to A. hydrillicola. Our results demonstrate that LAMP can effectively be utilized with crude DNA extracts to detect the cyanobacterial toxin gene clusters in the field at concentrations similar to conventional PCR. Once fully developed, this protocol could be used to create an AETX field test kit for scientists and managers to detect the potential for AETX, the eagle killer toxin.