Abstract Plant colonization in the archaeological areas, despite its relevant role for monument conservation, has not dedicated noticeable concern. For the first time in Iran, we carried out a floristic evaluation in an archaeological area and its biodeterioration hazard, choosing Pasargadae WHS. Among the 142 detected species, found in the 9 study areas of the site, 48 ruderal common species resulted widely distributed, with a dominance of grasses (mainly Therophytes and Hemicryptophytes) belonging to the Asteraceae and Poaceae families. The analysis of plant colonization identified 10 possible Micro-Sites of growth (MS = place of growth on stone observed at small scale), half of which are described for the first time. Besides the life forms of plants, plant colonization in specific MS was selected as a parameter for hazard evaluation. Then, we coupled this information with five determinant parameters for plant growths, having each one three classes of value to obtain the final evaluation. The colonization in joints and fractures of stone blocks, as well as the surface covered by soil, represent the highest hazard conditions for biodeterioration. Green-gray sandy limestone, which was used as a platform for palaces, had the highest colonization. The collected data will contribute to the site management.