The study was carried out to attract attention to the importance of holistic approach in ecological research studies and provide information about ecosystem qualification mapping, the fundamental layer for ecosystem-based management plans, by means of a case study example. In the study, species richness, potential energy footprint, resilience, rarity and dissimilarity were accepted as qualification components and the statistical analysis was performed by using 107 sample plot data taken from Yazili Canyon Nature Park, located in the transition zone of the Mediterranean region, Turkey. All components were calculated for each sample plot. Then, Principle Component Analysis (PCA) was applied to the components. As a result of the PCA applied, it was found that all components, except for dissimilarity, correspond with each other. Therefore, the formula for qualification index was created by taking species richness, potential energy footprint, resilience and rarity components into consideration. At the second phase of the study, qualification index and the dissimilarity component were modeled according to environmental factors taken as explanatory variables by using regression tree technique. With the regression tree models obtained, distribution maps of qualification index and the dissimilarity component were formed and group distinctions of the maps were drawn. Finally, by combining the groups of qualification index and the dissimilarity components, numerical values were assigned to the newly combined groups by using if-then rules. Thus, ecosystem based qualification value map of Yazili Canyon Nature Park was formed.