The aim of this paper is to analyze the effect of different degrees of mixing on the diversity structure in stands left to spontaneous development. The research included two communities of species endemic to the Balkan Peninsula—the Serbian spruce (Picea omorika Pančić Purk.) and the Macedonian pine (Pinus peuce Griseb). Data from eight sample plots were used in the research. The changes in diameter and height structure, spatial arrangement of trees, and diameter differentiation were analyzed. The analyzed parameters of structural diversity show relatively low to moderate values. Results showed an increase in mixing was reflected in the width and shape of distributions. A spatial analysis of stands with a higher degree of mixing showed a tendency towards a random to regular distribution of individuals, in contrast to stands with a lower degree of mixing which showed a tendency towards a clump distribution. The pronounced species’ dimensional and spatial diversity confirms their importance to the condition of modern forest management. Significant differences in the change of structure are shown by stands with a share of admixed species of above 20% by volume. The obtained results refer to stands left to spontaneous development, suggesting than an active research and management approach must be assumed to realize the goal of protecting rare forest ecosystems.