Oxford Nanopore Technologies offers cutting-edge long-read DNA sequencing technology that enables rapid, portable and accurate DNA sequencing of environmental samples in the field. We evaluated the efficacy of field-deployed Oxford Nanopore sequencing for analyzing environmental DNA (eDNA) while identifying gram-negative bacteria associated with upside-down jellyfish (Cassiopea xamachana) collected from Buttonwood Sound in Key Largo, Florida. The results shed light on microbial communities in this unique marine ecosystem, offering valuable insights into microbial interactions within Cassiopea.