Root rot and wilt disease complex was detected in several fig (Ficus carica L.), grapevine (Vitis vinifera L.), and pomegranate (Punica granatum L.) transplants in nurseries and new orchards of the El-Kharga, Baris, Balate, El-Dakhla, and El-Farafrah districts, of the New Valley governorate, Egypt. The percentage of root rot/wilt incidence and severity on fig, grapevine, and pomegranate transplants in the surveyed districts differed. The average percentages of root rot/wilt incidence and severity, in the surveyed districts, were 41.26, 31.42% in fig, 38.2, 29.5% in grapevine, and 32.1, 23.7% in pomegranate transplants, respectively. The most frequently isolated fungi from rotted roots of fig, grapevine, and pomegranate transplants were Fusarium oxysporum, Rhizoctonia solani, and Macrophomena phaseolina. In pathogenicity tests, all the tested fungi were pathogenic to fig, grapevine, and pomegranate transplants. Under laboratory conditions, all of the following tested bio-agents: Azotobacter sp., Bacillus cereus, B. megaterium, and B. subtilis, were able to inhibit growth of the causal pathogens to different degrees. The effect of these bio-agents individually and/or mixed, when used as a soil drench treatment, were varied in reducing the incidence and severity of root rot/wilt diseases in fig, grapevine, and pomegranate transplants under greenhouse conditions. The mixed bio-agents gave the highest protection against root rot/wilt diseases compared with the individually used of bio-agents. All treatments significantly increased plant height, number of leaves/transplant, leaf area, fresh and dry weight/transplant compared with the control treatment.