The microbiota of Pleuromamma species, an abundant genus of copepods that migrate vertically from surface waters to several hundred meters water depth and back on a daily basis was investigated along the Atlantic Meridional Transect using various molecular and morphological techniques. Sequencing of 16S rRNA amplicon libraries derived from individual Pleruromamma copepods showed a broad diversity of Bacteria associated with these copepods. Although various classes of bacteria were common (especially belonging to varius gammaproteobacterial genera), a prominent member of the associated bacterial community was identified as related to Limnobacter sp., Betaproteobacteria. Electron microscopy showed the presence of bacteria in the midgut region of the copepod guts and fluorescent in situ hybridisation with a Limnobacter-specific probe confirmed their presence in the gut of Pleuromamma copepods.