Cross-taxon analyses can explain patterns of interaction between taxa and their application in conservation studies can drive management actions. In a coastal sand dune system characterized by a high human pressure, we explored the co-occurrence patterns between vascular plants and bryophytes, with a focus on how the occurrence of invasive alien species (IAS) can affect those taxa and their relationships. Species congruences were evaluated at the community level considering taxonomic and functional diversities. Predictive co-correspondence analysis (Co-CA) was applied to quantify the strength of vascular plant communities in predicting bryophytes species composition. The relationship between the composition of vascular plants and bryophytes was significant, even if weak. Altitude and percentage of bare soil cover are the environmental variables exerting greater influence on the two taxa. The presence of IAS affects communities in an opposite way: for vascular plants, species richness increases with the presence of invasive alien species; for bryophytes, IAS’s presence has a low but significant negative influence, both on species richness and in terms of functional diversity. Results give elements for future studies on the effect of IAS on the bryophytes colonizing coastal sand dunes.