Organic chemical structures are known to be synthesized in laboratories or isolated from natural sources. Organic structures isolated from plants can be used as therapeutic and colorant in pharmaceutical, cosmetic, food and textile industries. In this study, powder thyme (Thymus Zygiodes) plant obtained from the markets of the Kayseri province. The extract of the plant with distilled water was prepared in 1:2 ratio. Agarose gel electrophoresis method was used to examine the interaction status of the extract substances and plasmid DNA (pBR322). The extract of thyme opened the supercoiled structure of plasmid DNA form I. Accordingly, the concentration of the form II structure increased. The nicked form II structure transformed into the form III linear DNA structure. In addition, the onion root cells that were incubated with the extract were imaged in three separate filters under fluorescent microscope. Since the purpose of the study was to investigate the fluorescent properties of the thyme extract and its interaction with DNA, it was determined that thyme extract has fluorescent substances and one of them interacts with DNA. However, it can be determined which substance it is with isolations, chromatographic and spectroscopic analysis. Thus, Thyme extract can be used as a DNA marker.