The conservation of coastal seascapes requires a better understanding of how different dimensions of biodiversity are represented between juxtaposed habitats. We explored patterns of taxonomic, functional, and phylogenetic diversity of fishes between four habitats (sandy bottoms, rocky reefs of high and low relief, and mixed bottoms) within a semi-lagoon seascape (Las Canteras beach) in Gran Canaria Island. Data on fish presence in each habitat were provided by weekly snorkeling tours, at day and night, from August 2015 to August 2018. Indices that measured ‘how much’ biodiversity, i.e., ‘how many species’ (species richness), ‘how much functional dissimilarity’, and ‘how much evolutionary history’ were larger on rocky bottoms. However, indices that measured phylogenetic differentiation, i.e., ‘how different’, via the taxonomic distinctiveness and the Mean Pairwise Distance index were particularly high on sandy bottoms, because of the presence of elasmobranchs, which were absent from rocky bottoms. The ‘phylogenetic signal’, whether phylogenetically related species are functionally similar, was significant on rocky bottoms, but non-significant on sandy bottoms, reflecting phylogenetic ‘overdispersion’ on sandy bottoms and phylogenetic ‘clustering’ on hard bottoms. From a conservation perspective, sandy bottoms cannot be underrated, particularly in the context of maximizing indices that measure ‘how phylogenetically different’ biodiversity is.