Archaeobotany is one of the disciplines within environmental archaeology focusing on the analysis of plant remains from archaeological sites. In general, archaeobotany comprises various study areas, which can be named differently according to the biological materials they analyze. The archaeological plant finds are classified as macro-remains (seeds, fruits, and charcoals) and micro-remains (phytoliths, starch, and pollens). Macro-remains are recovered, in most cases, by water flotation, which depends on separating the carbonized plants from the soil matrix through the flow of water. Other methods of recovery are also used according to the respective preservation conditions.

Current archaeobotanical studies cover a large number of research themes. Plant subsistence is widely addressed by archaeobotanists from the very beginnings of the discipline. Palaeovegetation and past environmental conditions are also regular subjects in archaeobotanical literature, especially through pollen and charcoal analyses. Fuel use is a part of the long-lasting discussion in archaeobotany in terms of dung burning as fuel and how to identify dung in the plant material. In the case of plant micro-remains, phytolith and starch analyses provide important information on past food habits.

The research goals of archaeobotanical research at Phoenix can be categorized within three interconnected themes: agroecology, plant biodiversity, and the use of natural resources. The agroecology theme will mainly target research questions related to crop production and past agricultural practices at Phoenix. This is an important research field to understand how past agricultural practices were organized and how ecological conditions of arable fields were during the occupation period. Agricultural terraces are conspicuous landscape features around the settlement hinting at human modification of natural landscapes to increase agricultural productivity. Furthermore, the other research themes will be plant biodiversity and exploitation of natural resources. The wider region shows an exceptional floral biodiversity with about 2000 taxa. Besides the presence of an endemic palm species (Phoenix theophrasti), Turkish sweetgum (Liquidambar orientalis) forms pure stands only in this region in the Eastern Mediterranean. Given this, documenting the ancient plant biodiversity through several lines of material evidence becomes an important task to understand how the ancient inhabitants of Phoenix exploited these floral resources.