The aim of the study was to isolate, characterize and identify pathogenic microorganisms and funqi from Hylocereus polyrhizous sp.( red dragon fruit ) in Kelantan. Pieces of tissues were collected from the lesion margins. After surface disinfestations with 1% sodium hypochioride for 1 min and rinsing in sterile water three times, the diseased tissues were placed on potato dextrose agar medium plates (PDA) and incubated at 28°C for 3 days. A dark, fast-growing fungus was isolated from all samples. For identification, single-spore cultures were grown on PDA in an incubator at 28°C. After 5 days, colonies with dark gray to black aerial mycelium formed. The colonies produce abundant conidia that occurred in arthric chains in aerial mycelium. Macroscopic and microscopic observations were carried out on pure isolates and observations were done based on Morpohology of Fungi (S.R. Misra, 2005). Fungi isolated were Aspergilus, Rhizopus, Penicilium, and Fusarium species. Pathogenicity test for the fungi were done by using modification of bioassay of fungicide — adaption of food poison technique. Three type of fungicide were used, Thiram, Dimethyldicarbonate and Zineb were compared with control PDA which not containing fungicide to determine the percentage of inhibition. Fungicide Thiram show the highest percent of inhibition compare to the Dimethyldicarbonate and Zineb.