Traditional classification systems represent cognitive processes of human cultures in the world. It synthesizes specific conceptions of nature, as well as cumulative learning, beliefs and customs that are part of a particular human community or society. Traditional knowledge has been analyzed from different viewpoints, one of which corresponds to the analysis of ethnoclassifications. In this work, a brief analysis of the botanical traditional knowledge among Zapotecs of the municipality of San Agustin Loxicha, Oaxaca was conducted. The purposes of this study were: a) to analyze the traditional ecological knowledge of local plant resources through the folk classification of both landscapes and plants and b) to determine the role that this knowledge has played in plant resource management and conservation. The study was developed in five communities of San Agustín Loxicha. From field trips, plant specimens were collected and showed to local people in order to get the Spanish or Zapotec names; through interviews with local people, we obtained names and identified classification categories of plants, vegetation units, and soil types. We found a logic structure in Zapotec plant names, based on linguistic terms, as well as morphological and ecological caracteristics. We followed the classification principles proposed by Berlin [6] in order to build a hierarchical structure of life forms, names and other characteristics mentioned by people. We recorded 757 plant names. Most of them (67%) have an equivalent Zapotec name and the remaining 33% had mixed names with Zapotec and Spanish terms. Plants were categorized as native plants, plants introduced in pre-Hispanic times, or plants introduced later. All of them are grouped in a hierarchical classification, which include life form, generic, specific, and varietal categories. Monotypic and polytypic names are used to further classify plants. This holistic classification system plays an important role for local people in many aspects: it helps to organize and make sense of the diversity, to understand the interrelation among plants–soil–vegetation and to classify their physical space since they relate plants with a particular vegetation unit and a kind of soil. The locals also make a rational use of these elements, because they know which crops can grow in any vegetation unit, or which places are indicated to recollect plants. These aspects are interconnected and could be fundamental for a rational use and management of plant resources.