The ecological relationships among six microencruster species from the Cipit boulders of the St Cassian Formation (Ladinian–Carnian of the Dolomites, NE Italy) were studied in detail. 112 thin sections in postcard format (10 × 15 cm) and in 7.5 × 10 cm from the localities Alpe di Specie and Misurina were taken into account. Initially, twelve microencruster species were found: Koskinobullina socialis, Terebella lapilloides, Tubiphytes obscurus, Baccanella floriformis, Reptonoditrypa cautica, Plexoramea cerebriformis, Ladinella porata, Microtubus communis, Pseudorothpletzella schmidi, Alpinophragmium perforatum, Planiinvoluta sp and Tethysocarnia cautica. A phenetic algorithm combining three cluster analyses in R‐mode (UPGMA, WPGMA and nearest neighbour) as well as two indices (Jaccard and Bray–Curtis) was performed on all samples. Six microencruster species – grouped in three pairs – were found to have high Jaccard and low Bray–Curtis values at all algorithms. These pairs are represented by Koskinobullina socialis – Pseudorothpletzella schmidi, Terebella lapilloides – Tubiphytes obscurus and Reptonoditrypa cautica – Baccanella floriformis, and were clearly recognizable as robust branches in all phenograms. A further index (Simpson's similarity index) was included successfully in the algorithm in order to sustain the robustness of these phena. This method proved to render reliable results and could be successfully applied in all reef and reef‐like fossil ‘communities’, with the aim of establishing the palaeoecological implications and the specific constraints of selected microencrusters.