<p>Vanilla is one of the important agricultural export commodity of Indonesia. The vanilla from Indonesia is well known for it high levels of vanillin content,which is about 2,75%. Until recently, the most hazardous disease of vanilla is foot rot infection caused by Fusarium oxysporum f. sp.vanillae (Fov). One alternative way to control the foot rot disease is by using cultivars which resistant to its pathogen. Selected plantlets have been induced by using fusaric acid on the in vitro medium. The goal of this research is to characterize the anatomical point of few especially on leaves, pseudo bulb and root with respect of resistant to Fov. Moreover, it is also addressed to determine the different characters of the phenotype vanilla plantlet whichare total of phenol, peroxydases enzyme activity, the thickness of lignin, and the chlorophyll content. The data on this research were recorded, compiled and categorized as descriptive qualitative and quantitative information. Theresult showed significant increase in chlorophyll a, chlorophyll b, and also the total of chlorophyll. The overall in line correlated with the increasing FA concentration. The total chlorophyll at 90 ppm FA could increased about 1,2 times, while at 100 ppm and 110 ppm FA could enhanced about 1,4 to 1,5 times compared to control. Anatomical characters between vanilla control, infected fov, and resistant to fov, were showed clearly at the stele part especially at xylem as the main function for transporting water from root to the leaf, which formed thyllose. Phenol total at about 4,39 % in control, increased to 5,34% in 90 ppm, and followed by 5,52 % in 100 ppm and 5,87 % at 110 ppm. Peroxidases enzyme activity at FA 90 ppm produced about 0,25 U/mg/min, and at 100 ppm FA on 0,34 U/mg/min, while at FA 110 ppm generated 0.36 U/mg/min compared to control, at 0,12 U/mg/min. The thickness of lignin tracheid in the treatment of 90 ppm was at about 14,59 ìm; 100 ppm 18,16 ìm; and 110 ppm 19,39 ìm compared to controls 10,28 ìm. In conclusion over all showed that FA induced plantlet vanilla inin vitro medium resulted in change of phenotype compare to control, which also affect its anatomy structure, especially on lignification and thyllose formation at surrounding tracheids, which could be use as marker for defend mechanism of plant to Fov.</p><p><br /><strong>Keywords</strong>: Fusarium oxysporum f. sp.Vanillae, peroxydases enzyme, anatomical characters.</p>