The Hyrcanian Forests, well-known for its World Heritage site in the South Caspian region of Northern Iran, are refugia for a special tree flora. Some areas in particular feature a concentration of large and numerous trees of Taxus baccata, a species that has attracted the interest of many researchers given its medicinal importance. The objective of this study was to analyze the biological and structural features of these unique ecosystems based on three large tree-mapped field plots using new methods. We developed a species abundance distribution and three species–area relations, and analyzed the small-scale structural patterns of each of the 15 tree species that occur in the plots. Species-specific details are presented for each of the three field plots, including the tree densities and average tree sizes, as well as the associated structural indices “species mingling”, “dominance”, and “size differentiation”. This includes non-linear relationships between tree density and neighborhood mingling, and between the average tree size and neighborhood dominance, and a linear relation between the neighborhood dominance and the mean neighborhood differentiation. Based on the findings, we recommend the use of these methods and indices for analyzing the structure of natural forests in other regions of the world.