The batik industry in Yogyakarta is mostly found in small or medium scale industries. This condition results in a limited capacity for waste processing. Batik wastewater contains various types of heavy metals such as chromium, aluminium (Al) and iron which can be dangerous to the environment. Marigold (Tagetes erecta L.) as a member of the Asteraceae family is known to have potential as a phytoremediator plant of various types of metals. This study aimed to determine the anatomical responses of T.erecta L. roots and stems to the batik wastewater exposure. The concentration of waste used were 0%, 25%, 50%, 75% and 100%. The treatment was done every five days for 25 days according to field capacity to one and a half months old plants. Parameters observed were plant morphology, plant growth, root and stem anatomy. The preparation of transverse section of roots was carried out by paraffin embedding method, while the transverse section of stems was prepared by non-embedding method. The results showed that there was a decrease in plant height, roots volume, root length, and plant biomass along with increasing concentration of the wastewater given. The leaves growth increased most rapidly at 25% waste. The treatment of 50% to 100% waste caused leaf chlorosis and necrosis and damage to the root epidermis and cortex cells as seen by cells shape, from round or pentagonal or hexagonal to ellipsoid cells. The highest values of root, stele, and trachea diameters, as well as cortex thickness, were obtained in the concentration of 50% while the lowest was found at 100%. The stem diameter increased up to 50% treatment with the highest value and then decreased by 75% and 100% waste. The stem epidermis thickness, cortex thickness, and vascular tissue were reduced in treated plants, with the lowest was found in 100%.