In Ecuador, there is a progressive loss of the native forest. To mitigate these problems, several reforestation plans have been carried out in the country. To recover the Andean forest, Polylepis racemosa was introduced from Peru, due to its similarity to native species like Polylepis incana. This genus fulfills important ecological functions that help mitigate the effects of local climate change. However, reforestation of introduced species close to natural populations threatens the genetic diversity of Polylepis native forests. In the long term, it can trigger hybridization processes and create problems for ecosystem conservation. This study used geometry morphometric (GM), to differentiate species quickly and economically, using the form of leaves, stomata, flowers, and pollen of P. incana and P. racemosa in three populations: Illinizas Ecological Reserve, Mojanda Lagoons and Cayambe-Coca National Park. To obtain the data, the composite leaves were scanned, the stomata and pollen were photographed with an increase of 400× and on flowers with 100×. 15, 10, 12, and 9 landmarks (LM) were digitized for leaves, stomata, flowers, and pollen, respectively, using ImageJ software. Then, the shape variables and statistical analysis were performed in MorphoJ software. As a result, it was obtained that the discriminant function analysis (DFA) shows that leaves and flowers can be used as indicators to differentiate species from this genus, discarding stomata and pollen. After that, Canonical Variate Analysis (CVA) of leaves and flowers showed that reforested species jointly are separated into two different species; except for the flowers of the population of Mojanda, where there is an intersection of few individuals, which share similar phenotypic characteristics so they can be considered as potentially hybrid individuals. This study generates information on the location of species introduced inside and outside the National System of Protected Areas that threaten the Andean highlands. Finally, GM is an accessible tool for monitoring biodiversity through morphological characteristics and discriminating against species with complex taxonomic problems.