A study on the type and distribution of trichomes, morphological traits of the calyx and content of antioxidant compounds was conducted on Teucrium arduini L. populations in Croatia and in Bosnia and Herzegovina. Non-glandular trichomes, peltate trichomes and small capitate trichomes with four secretory head cells were observed on leaves, stems and calyx, whereas long capitate trichomes with a unicellular head cell were observed exclusively on the calyx. Average calyx length was 5.23–6.51 mm, calyx tube length 2.92–3.68 mm, lower lip length 1.25–2.42 mm and upper lip length 1.89–2.99 mm. The concentration of antioxidant compounds in all populations was the highest in leaves: total polyphenols (TP): 8.43–13.55%; tannins (T): 1.79–7.33%; flavonoids (TF): 0.28–0.40%; phenolic acids (TPA): 2.90–5.07%. Inflorescences generally contained the smallest amount of TP (5.89–11.42%), T (0.87–6.50%) and TPA (1.66–2.27%), while the smallest content of TF was obtained for the majority of stem samples (0.06–0.12%). The researched populations did not differ with regard to the type and overall distribution of the trichomes, though the Bosnian populations have a shorter calyx tube and longer upper lip. Some variability was observed in the TP and T content between sampling sites, while quite high variability was noted in the TF and TPA content.