Dinoflagellates and bacteria are fundamental components of the marine pelagic ecosystems. In the marine environment they can develop close associations that might lead to complex interactions. These interactions can be observed as either nonspecific interactions or algal-bacterial symbiotic interactions. Generally the relationship between dinoflagellates and associated bacteria is postulated to be 'symbiotic' when both organisms coexist without apparent symptoms and in some cases the association is maintained for a long time. The dinoflagellate associated bacteria (DAB) play an important role as algal growth and bloom dynamics regulators. There is a growing list of studies of bacteria associated with harmful algal species, especially within the dinoflagellate group. The bacterial groups most often associated with dinoflagellates and diatoms are alpha Proteobacteria, gamma Proteobacteria, beta Proteobacteria and cytophaga-flavobacteria-bacteroids. Within gamma Proteobacteria, Marinobacter spp. are known to stimulate dinoflagellate growth. The localization and identification of specific groups of DABs are important to evaluate the role of bacteria-dinoflagellate associations in marine ecosystems and to reach a better understanding of toxic bloom dynamics. Various microscopy techniques have been used to assess the physical association between these two organisms. Moreover there are different molecular biology techniques like fluorescent In-situ Hybridization (FISH) which have been used to identify DABs. However both these techniques when used separately cannot provide a simultaneous identification and localization of DABs. For this purpose, in situ hybridization using oligonucleotide probes targeting 23S/16S rRNA combined with a precise detection method such as confocal laser scanning microscopy (CLSM) has been proved to be a useful technique. The aim of this research work is to identify and localize bacteria associated with dinoflagellates using different microscopy techniques such as scanning electron microscopy (SEM) and CLSM coupled with FISH. The bacteria were successfully hybridized with HRP labeled GAM42a probe (specific for gamma Proteobacteria) in the laboratory culture of Scrippsiella trochoidea. The hybridized bacteria were also abundant in the environmental samples collected at Scripps pier, La Jolla, CA. Thus SEM and CLSM studies confirmed the close association of this dinoflagellate with the gamma Proteobacteria. The tyramide signal amplification (TSA) system associated with FISH allowed a clear identification of bacteria attached and associated with dinoflagellates when using the general gamma Proteobacteria probe. This study has demonstrated the use of enzyme (HRP)- oligonucleotide probe conjugates for specific hybridization to intracellular rRNA within bacterial cells. We are continuing to evaluate more specific enzyme probe conjugates in specific bacteria of interest which will provide a valuable tool for the detection and identification of specific bacterial strains in situ.