Here we present the methodology used for terrestrial biodiversity analysis and site selection in Phase B of the UNDP/GEF COAST project. The analysis was focused on the problem of biodiversity evaluation in four Croatian counties stretching from sea level to the highest mountain in Croatia. Data on habitats, vascular flora, and fauna (mammals, birds, reptiles, amphibians, butterflies, ground beetles, and underground invertebrates) were collected and analyzed for each of the four counties. Emphasis was given to the richness of endangered species and the rarity of endemic species. Based on the spatial analyses of habitat, fauna, and flora data, four to six areas were selected from each county and ranked according to their biodiversity importance. Overlap between areas important for richness and those important for rarity was highest for data on flora (65.5%) and lowest for data on fauna (16.7%). When different data sets were compared, the lowest overlap was between flora and fauna (17.1%) and largest between fauna and habitats (23.9%). Simultaneous overlap among all three data sets was found in just 6.5% of the overall selected areas. These results suggest that less specific data, with respect to taxa threat status, could better serve as surrogate data in estimating overall biodiversity. In summary, this analysis has demonstrated that Dalmatia is a region with a high overall biodiversity that is important in a broader European context.