Linear and geometric morphometrics approaches were conducted to analyze the head capsule (HC) shape of collected soldier caste specimens of Coptotermes from various locations in Indonesia. The soldiers’ morphology was observed and measured. The results of the principal component analysis of the group of all species showed two important groups of variables, i.e., the body size and setae characteristics of the pronotum and head. The multicollinearity of the morphometric variables showed the importance of body measurements as well as important alternative characteristics such as the pronotum setae (PrS) and HC setae. Four trends of HC shape were observed across the species. Interestingly, three extreme shapes were depicted by geometric morphometrics of the C. gestroi HC. The phylogenetic tree inferred from 12S and 16S mitochondrial gene fragments showed high confidence for C. gestroi populations. The lateral expansion of the posterior part of the HC across the species was in accordance with the increasing of the number of hairlike setae on the pronotum and HC. These differences among species might be associated with mandible-force-related defensive labor and sensitivity to environmental stressors.