Toxigenic benthic dinoflagellates of the genus Prorocentrum interact with bacteria. The nature of the interactions may avoid or trigger a benthic harmful algal bloom and/or be related to toxin production and cell survival. In this study, the bacterial communities of xenic Prorocentrum isolates originated from Mexican coastal waters were analyzed in the culture medium-associated and host-associated fractions by V3V4-16S amplicon sequencing to define the community composition, core members, and potential metabolic functions.