We studied species richness patterns of obligate subterranean (troglobiotic) beetles in the Dinaric karst of the western Balkans, using five grid sizes with cells of 80 × 80, 40 × 40, 20 × 20, 10 × 10, and 5 × 5 km. The same two hotspots could be recognized at all scales, although details differed. Differences in sampling intensity were not sufficient to explain these patterns. Correlations between number of species and number of sampled localities increased with increasing cell size. Additional species are expected to be found in the region, as indicated by jackknife 1, jackknife 2, Chao2, bootstrap, and incidence-based coverage (ICE) species richness estimators. All estimates increased with increasing cell size, except Chao2, with the lowest prediction at the intermediate 20 × 20 km cell size. Jackknife 2 and ICE gave highest estimates and jackknife 1 and bootstrap the lowest. Jackknife 1 and bootstrap estimates changed least with cell size, while the number of single cell species increased. In the highly endemic subterranean fauna with many rare species, bootstrap may be most appropriate to consider. Positive autocorrelation of species numbers was highest at 20 × 20 km scale, so we used this cell size for further analyses. At this scale we added 137 localities with less positional accuracy to 1572 previously considered, and increased 254 troglobiotic species considered to 276. Previously discovered hotspots and their positions did not change, except for a new species-rich cell which appeared in the south-eastern region. There are two centres of troglobiotic species richness in the Dinaric karst. The one in the north-west exhibited high species richness of Trechinae (Carabidae), while in the south-east, the Leptodirinae (Cholevidae) were much more diverse. These centres of species richness should serve as the starting point for establishing a conservation network of important subterranean areas in Dinaric karst.