Predicting ecosystem functioning requires an understanding of the mechanisms that drive microbial community assembly. Many studies have explored microbial diversity extensively and environmental factors are thought to be the principal drivers of community composition. Community assembly is, however, also influenced by past conditions that might affect present-day assemblages. Historical events, called legacy effects or historical contingencies, remain poorly studied in the sea and their impact on the functioning of the communities is not known. We tested the influence, if any, of historical contingencies on contemporary community assembly and functions in a marine ecosystem. To do so, we verified if different inoculum communities colonizing the same substrate led to communities with different compositions. We inoculated wood with sea water microbes from different marine environments that differ in ecological and evolutionary history. Using 16S rRNA and metagenomic sequencing, it was demonstrated that historical contingencies change the composition and potential metabolisms of contemporary communities. The effect of historical events was transient, dominated by environmental selection as, over time, species sorting was a more important driver of community assembly. Our study shows not only that historical contingencies affect marine ecosystems but takes the analysis a step further by characterizing this effect as strong but transient.