An increase in wastewater rejection and rising seawater temperature are the two main causes of the spreading of pathogenic bacteria in the ocean that present a risk to the health of marine organisms, i.e., corals. Deciphering the infectious mechanism is of interest to better disease management. The quantity of infecting bacteria as well as method of pathogen administration is an important parameter in studying host-pathogen interactions. In this study, we have tested two models of infection (bathing or injection) of Exaiptasia diaphana (E. diaphana) with a clinically isolated strain of Vibrio parahaemolyticus expressing constitutively a Green Fluorescent Protein (Vp-GFP). We followed Vp-GFP dissemination over time with confocal microscopy at 6, 24, and 30 h. During the early time of infection, bacteria were observed adhering to the ectoderm in both infection methods. In later stages of the infection, Vp-GFP were lost from the ectoderm and appeared in the gastroderm. Compared to bathing, the injection method was supposed to provide better control of the bacteria quantity introduced inside the animal. However, injection induced a stress response with contraction and rejection of bacteria thus making it impossible to control the number of infecting bacteria. In conclusion, we recommended using the bathing technique that is closer to the infection route found in the environment and, moreover, did not cause injury to the animal. We also demonstrated, by using Vp-GFP, that we could track pathogenic bacteria in different tissues of E. diaphana over the time of infection and quantify them in the whole animal, thus opening a technical approach for developing new strategies to fight infection disease.