The Convention on Biological Diversity (CBD) defines biological diversity as the variability among living organisms from all sources including, inter alia, terrestrial, marine and other aquatic ecosystems and the ecological complexes of which they are part; this includes diversity within species, between species and ecosystems. Hence, a country or a region becomes biodiverse, when it contains much of the world's species (endemicity)--be it in terms of genetic, habitat or species diversity. In essence, it then becomes a biodiversity hotspot when it has lost or continuously loses its biodiversity.
To date, approximately 1.5 million species have been named, but there are more still unnamed and undiscovered. This concerns one of the questions I've posted here (What do you think will happen to biodiversity in the next 50 years) because if majority of the species remains unaccounted, then we might not even know what we are losing or worse have already lost them before we even discover them.