The botany department of the Natural History Museum began its activity in 1353 with a few plant samples. Over time, it expanded by collecting plant samples from different regions of the country, particularly Fars province, beginning in 1364. The museum's herbarium now contains 4560 scientifically identified and classified plant samples.

The activities of the botany department are conducted and showcased in three main parts: research, education, and demonstration. The educational and plant demonstration sections of the museum consist of various parts, such as:

Plants in the Qur'an, Medicinal plants, Plants in Iranian literature, Educational boards, Dried Plants in their natural form, Types of blooming and non-blooming fruits, leaf types, distribution of seeds, Examples of Iranian vegetation(ornamental plants, Iranian astragalus, wheat, etc.), Conjoined twins in the plant world.