The rising impact of invasive species and climate change on Mediterranean fish biodiversity highlight the urgency to evaluate the current status of natural assemblages. Here we investigated the rocky-reef fish of Malta and Lampedusa (Strait of Sicily, Mediterranean Sea), two islands of high biogeographical importance subjected to a different level of protection and anthropic pressure. By using underwater visual census, a total of 192 counts were performed in May-June and September-October 2007 using a hierarchical spatial design and four depth layers. Overall, 23 families and 61 different taxa were recorded. Out of them, two highly invasive species were censused (i.e. Siganus luridus and Fistularia commersonii) with relatively low abundances. Native Labridae and Sparidae shape the assemblage structure of both islands, and thermophilic species such as Sparisoma cretense and Thalassoma pavo occur with high densities. The fish assemblages of Malta and Lampedusa were relatively similar in species composition, richness and total abundance. Nevertheless, multivariate analysis depicted significant differences between these two islands, mainly attributable to the unevenness of Labridae. Significant differences in the size distribution of the most abundant species were detected between islands, with parallel variation across time. The pattern of spatio-temporal variability of the whole assemblage structure strongly resembled that of nekto-benthic fish, hence pointing out the relevance of this guild as an indicator species group in future monitoring activity. This study will serve as a current baseline against which future changes in the central Mediterranean fish assemblages can be assessed. © Marine Biological Association of the United Kingdom, 2013.

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