Several researchers have previously claimed to produce axenic Alexandrium cultures and used them in various studies, including investigations of bacterial effects on dinoflagellate toxicity. However, production of these cultures and ensuring their axenic status is a notoriously difficult task. This paper presents data detailing the effects of different antibiotic and chemical (EDTA, lysozyme and SDS) treatments on dinoflagellate microflora and highlights the pitfalls of these approaches. Particularly resistant isolates may be capable of assuming a cryptic form which can recolonise dinoflagellate cultures upon removal of antibiotics and chemicals. Results suggest that certain species within the bacterial consortia of both toxic and non-toxic dinoflagellates may constitute a crucial symbiosis. Therefore, the reduced bacterial community from treated dinoflagellate cultures has been characterised and compared with the original microflora in untreated cultures.