Thraustochytrids, important decomposers in marine ecosystems, exhibit complex life cycles and are prolific producers of bioactive compounds, including polysaccharides, enzymes, pigments, lipids, fatty acids, squalene, and DHA with high application valuable. Taiwan, encompassing diverse thraustochytrid habitats, potentially hosts a variety of species. In this study, morphological traits and molecular analysis were used for identification of six isolates included Botryochytrium sp., Parietichytrium sarkarianum, Schizochytrium sp., Thraustochytrium aureum, Thraustochytriidae sp., and Ulkenia visurgensis. The vegetative cells, ectoplasmic networks, and flagellated zoospores of T. aureum, U. visurgensis, and P. sarkarianum were observed through dissecting, light and scanning electron microscopy. The globular vegetative cells of T. aureum displayed slight branching and protrusions in their ectoplasmic networks. The protoplast of P. sarkarianum are released from a vegetative cell and migrated outwards to form zoosporangium. Ulkenia visurgensis has globular, thin-walled or thick-walled vegetative cell. We assessed their osmotic tolerance and antibacterial properties. The thraustochytrids isolates displayed no antagonistic interactions with various bacteria, including Vibrio spp., Klebsiella spp., Listonella anguillarum, Staphylococcus aureus, Salmonella enterica, and Escherichia coli.