We transplanted oysters from two invasive, genetically distinct invasive populations of the Wadden sea (Texel, Netherlands and Sylt, Germany, and monitored the short term microbiota shifts and colonization in different tissues during the initial phases of establishment in the new habitat. To manipulate the microbiome mismatch we treated half of the oyster with antibiotics in order to minimize the interactions between resident microbiota and new colonizers, while the other half was transplanted with their natural resident microbiome. We followed oyster survival and changes in diversity, composition and abundance of oyster-associated bacterial communities as a whole and Vibrionaceae and Arcobacter in particular, over the first five days in the new habitat. In this way, we could estimate how the composition and diversity of microbiota in different tissues contribute to success of oyster establishment in the new environment.