Fluorescent labeling of bacterial isolates is a powerful tool to microscopically explore the spatial  and  temporal  dynamics  ofhostbacterial  colonization. Bacterial  cell  labeling  has become prevalent in medical and plant research(Gilbertson et al., 2007; Aymanns et al., 2011), but marine host-bacterial dynamics remain largely underexplored. Thus, even though coral microbiome manipulation was shown to effectivelyimprove coral heat stress recovery, the underlying mechanisms remain elusive due to a lack of methods to query bacteria-host and bacteria-bacteria associations. Critical to fully grasp probiotics as an active intervention is an  understanding  of  colonization  success,  residency,  and  spatial  assemblage  of target bacteria. Here,we present a broadly applicable protocol to transform bacterial isolates with fluorescent reporter-carrying plasmids(here: pRL153-GFP) (Tolonen, Liszt and Hess, 2006). Our protocol is based on previous approaches in the freshwater polyp Hydra(Wein et al., 2018)and the tubeworm Hydroides  elegans(Alker et  al.,  2023). Using  this  protocol,  we successfully conjugated a broad taxonomic range of marine bacterial isolates from the coral model Aiptasia using E. coliMFDpirΔDAPWM3064cells (Ferrières et al., 2010)as plasmid donors. Additionally, we visualized GFP-carrying bacteria in culture and in hospiteon Aiptasia polyps after bacteria incubation. We are currently conductingdetailed studiesof colonization dynamics and localization of fluorescent bacterial isolates following microbiome manipulation. We hope the here-developed protocol will be useful for researchers studying host-microbiome interactions and the mechanisms underlying microbiome-mediated host resilience.