Wild Indian plum (Ziziphus zizyphus), locally known as ‘angkil’, is a rich source of vitamin C and contains minerals and proteins. The ripe fruits are mostly consumed fresh. Processed products like candy, pickle, chutney and jelly are also prepared from fruits. The young plants are used for making hedges and leaves are used as fodder. The objective of the study was to identify the disease causing pathogens in Z. zizyphus and soil microbes inhabiting the rhizosphere of this plant in the three zones of Nokrek Biosphere Reserve, as well as to assess the relationship between soil microbes and occurrence of plant pathogens. Eight diseases caused by fungal pathogens and one disease caused by algae were observed. Change in zone showed significant influence on occurrence of plant pathogens. Occurrence of soil microbes in the rhizosphere was significantly influenced by change in soil depth and season. Soil microbes were found to be more in top soil than subsoil. Soil microbes Fusarium oxysporum and Phytophthora palmivora inhabiting the rhizosphere of Z. zizyphus at 0–15 cm soil depth had a significant positive association with plant pathogens, Colletotrichum acutatum, Cercospora ziziphii and Cladosporium ziziphii while exerting an antagonistic effect on pathogens like Oidium erysiphoides, Colletotrichum gloeosporioides and Alternaria alternata. Soil microbe Penicillium terrestre at 0–15 cm soil depth showed significant association with pathogens O. erysiphoides and C. gloeosporioides. Soil microbes at 15–30 cm soil depth had no significant influence on occurrence of plant pathogens.