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ABSTRACT The generaParamoebaandNeoparamoeba, within the family Paramoebidae (order Dactylopodida), are distinguished by their dactylopodial pseudopodia and the presence of an intracellular eukaryotic symbiont, thePerkinsela‐like organism (PLO). Taxonomic classification within these genera has been challenging due to overlapping morphological traits and close phylogenetic relationships.Theyare marine, with some playing significant roles as parasites. Notably, they have been implicated in sea urchin mass mortality events and are known causative agents of Amoebic Gill Disease (AGD) in fish. Despite their ecological and economic importance, many aspects of their diversity, biology, evolution, and host interactions remain poorly understood. In this study, we describe a novel amoeba species,Paramoeba daytonin. sp., isolated from Daytona Beach, Florida. Morphological and molecular analyses confirm its placement within theParamoebaclade, closely related toP. eilhardi,P. karteshi, andP. aparasomata. Phylogenetic assessments using 18S rDNA (18S) and Cytochrome c Oxidase I (COI) markers demonstrate the limitations of the 18S gene for species delineation, highlighting COI as a more reliable genetic marker for this group. Additionally, observations on PLO morphology, movement, and microtubule association provide insights into the endosymbiotic relationship, reinforcing the need for further research into this unique eukaryote‐eukaryote symbiosis.