The dinoflagellate Prorocentrum lima is known to produce diarrhetic shellfish poisons. However, it is yet unclear if the dinoflagellates themselves or the bacteria associated with them produce the toxins. Here we analyze the toxicity as well as the spectrum of bacteria in two cultures of P. lima, namely P. lima-SY and P. lima-ST, which initially derived from the same P. lima strain PL2V. Toxicity tests, applying the Artemia bioassay revealed in both cultures high levels of toxins. The bacteria, associated with the two cultures, were identified by PCR/nucleotide sequence analysis of the 16S rRNA gene. From cultures of P. lima-SY the dominant sequence was found to share a 93.7% similarity with the sequence of Roseobacter algocolus [R. algicola]; the relative abundance was determined to be 83%. In addition three further sequences of bacteria, grouped to the α-Protobacteria have been identified: Paracoccus denitrificans [90.8%], R. algocolus [94.4%] and Rhizobium huakuii [92.6%]. The identification of bacteria in P. lima-ST revealed that most share highest similarity with Bartonella taylorii but with a relatively low score of 87%. In addition to this sequence, two sequences with high similarity to the genus Roseobacter were obtained. The other sequences identified have not been detected in P. lima-SY. Studies with pure bacterial strains, previously isolated from a culture of P. lima-ST and subsequently cultured on agar plates, revealed that none of them was identical to those identified in the dinoflagellate culture itself. An explanation for the change of the spectrum of bacteria in the different cultures can only be expected when axenic cultures from P. lima are available.