Pyrodinium bahamense var. compressum is a toxic dinoflagellate that produces paralytic shellfish poisoning toxins. It is responsible for the chronic toxicity of shellfish in many coastal areas of the Philippines and other South East Asian countries. For the purpose of using antibiotic treatment to possibly generate axenic cultures and understand their growth requirements, the antibiotic tolerances of two local P. bahamense var. compressum isolates and their associated bacteria were determined. The antibacterial compounds ampicillin, chloramphenicol, ciprofloxacin, kanamycin, neomycin, penicillin G, and streptomycin were tested, as well as two antifungals, amphotericin B, and nystatin. All except chloramphenicol, amphotericin B, and nystatin were generally well-tolerated. An antibiotic mixture composed of ciprofloxacin, kanamycin, neomycin, and streptomycin completely inhibited the cultivable bacteria associated with P. bahamense var. compressum MZRVA, although epifluorescence microscopy revealed that residual bacteria were still present. From long-term tests with this antibiotic mix, it was observed that survival of isolate MZRVA post-antibiotic treatment appeared to be associated with re-growth of heterotrophic bacteria and that excess vitamins could potentially enhance dinoflagellate survival. These results suggest that the associated heterotrophic bacterial populations help support the growth of P.bahamense var. compressum MZRVA in culture and possibly in nature. This is the first report on the growth responses of P. bahamense var. compressum and associated cultivable bacteria to a variety of single and combinations of antibiotics.