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Diversity indexes were calculated using the floristic data from the inventory. Beta diversity (β) was estimated using hierarchical cluster analysis, using Sorensen distance (Bray-Curtis). This distance was estimated as the floristic similarity among the identified groups with the previous analysis calculated with Jaccard's index for qualitative data and the Morisita-Horn index for quantitative data. To identify the indicator species of each one of the identified groups through the cluster analysis, the Dufrene and Legendre method was used [20]. Diversity alpha (α) was calculated with the reciprocal of Simpson index (C inv.) [21], and an unbiased estimator of diversity was calculated using the jack-knife technique. The horizontal structure was described with the relative values of abundance, dominance, and frequency of each species. In addition, the tree diametric class distributions were described for each plot. The ecological importance index value (IVIE), was calculated for each species as the sum of the parameters in the horizontal structure [22]. To describe the relationships among the variables, a principal components analysis (PCA) was performed, while to determine the association among environmental variables with the distribution and abundance of species for plots a canonical correspondence analysis (CCA) was done. Key or vulnerable species for high-priority consideration in restoration programmes were identified based on their abundance, dominance, commercial wood potential, and dasometric variables. The design of the restoration proposal was based on the approaches of [5] who suggest 13 steps for restoration strategies. 3. Results 3.1. Study of case No. 1: Mesophyll semi-deciduous forest of the Biosphere Reserve "Sierra del Rosario" (BRSR) We identified 36 families, 75 genera, and 91 species, with a total of 7,799 individuals registered from 30 sampled plots. The endemism rate was 11.24%, a similar value reported for the Biodiversity in Ecosystems-Linking Structure and Function 4 Alibertia edulis (L. C. Richt.) Acacia mangium Willd Bursera simaruba L. Sargent. Calycophyllum candidissimun (Vahl) DC. Andira inermis (W. Wright) Kunth Casearia hirsuta Sw. Cinnamomun elongatum (Nees) Kostermans Anonna reticulata L. Comocladia dentata Jacq Cochlospermun vitifolium (Willd.) Bambusa vulgaris Schrader ex Wendland Cupania americana L.