Although a number of recent studies have demonstrated biotic homogenization, these have mainly focused on larger spatial scales. Homogenizing effects are equally important at finer resolutions, e.g. through increasing similarity between habitats, which may result in a simplification of ecosystem structure and function. One major cause of homogenization is the expanding ranges of alien species, although it is not clear whether they are inherently homogenizing at smaller scales. We therefore assessed whether the alien flora is less complex across habitats than the resident native flora of Mediterranean Islands. From a regional data base, we examined floristic lists for between-habitat taxonomic and functional similarity, and within-habitat functional diversity, using resampled data sets to control for sample size biases. Aliens and natives showed equivalent complexity in most respects. At the taxonomic level, between-island and between-habitat similarities were almost identical, and when ecosystem function was measured by a functional group classification system, this was also true of between-habitat similarities and within-habitat diversities. When ecosystem function was measured using Grime's CSR classification, aliens were found to be more functionally homogenous between-habitats and less functionally diverse within habitats. However, since the CSR profiles of aliens and natives differed, simplification is not inevitable due to ecological segregation of the two floras (aliens tend to be recruited to disturbed habitats rather than displacing natives). One deficiency is a lack of large scale species abundance data. A simple simulation exercise indicated that this is likely to lead to substantial overestimation of true levels of similarity, although would only influence the comparison between aliens and natives if they have different abundance distribution curves. The results indicate that alien floras are not intrinsically more simple than natives, but a higher proportion of competitive strategists among aliens may still cause small-scale homogenization as these include many strong competitors that are likely to dominate communities.