The biotic diversity of Strombus gigas has not been thoroughly studied despite the status of the queen conch as an important ecological resource. The bacteria associated with the conch influence their host in several ways, including through the metabolism of nutrients, protection against invasive bacteria and the regulation of the physical conditions. In this study, conventional microbiological methods and molecular tools such as denaturing gradient gel electrophoresis (DGGE) were used to assess the composition of the bacterial communities associated with the queen conch (S. gigas) in wild and captive habitats in Colombia. A genetic analysis of the bacterial communities revealed a high level of diversity based on the large number of bands detected using DGGE. In addition, differences in bacterial community structure were found between the conchs in captivity and the wild populations. The dominant phylogenetic affiliations of the bacteria, as determined using 16S rRNA gene sequencing, were grouped into four classes, namely, Betaproteobacteria (16%), Gammaproteobacteria (70%), Firmicutes (7%) and Actinobacteria (2%). These groups are related to host defence processes and the decomposition of organic matter. The 16S rDNA sequence analysis of the cultured bacteria and the resulting DGGE profiles are useful tools for characterizing the diversity of the bacteria associated with the analyzed conchs.