Bell pepper (Capsicum annuum L.) belongs to family ‘Solanaceae’ is among the most popular and highly profitable vegetable throughout the world. Among various biotic constraints fruit and root rot fungal pathogens contribute the most in reducing the bell pepper produce qualitatively and quantitatively throughout the worldwide including Pakistan. No detailed studies prior to this work have been conducted in Pothohar plateau, Punjab, Pakistan. Consequently, there was a dire need to conduct a comprehensive study for documenting prevalence and incidence of fruit and root rot diseases. Moreover, fungicides are being used extensively against the disastrous fruit and root rot pathogens. These fungicides not only contaminate the environment but also are health risk for human beings. During 2015-16 and 2016-17 bell pepper cropping season, extensive surveys were conducted in 9 tehsils/territory of Attock, Chakwal, Jhelum, Rawalpindi and Islamabad territory. A total of 8 greenhouses and 45 farmer’s fields/low plastic tunnels were visited at seedling and maturity stage to document fungal pathogen associated with fruit and root rot of bell pepper and their incidence. The survey revealed four pathogens viz. Colletotrichum, Fusarium, Botrytis, and Alternaria were found responsible for fruit rot in bell pepper. In greenhouse, Botrytis was mainly found associated with fruit rot with 15.13 percent fruit rot incidence (%FRI) followed by Fusarium (13.63%) and Alternaria (9.69%). In open fields the Colletotrichum (20.73%) was mainly found associated with fruit rot, followed by Fusarium (12.04%), Alternaria (8.92%) and Botrytis (6.73%). Three pathogens viz. Fusarium, Rhizoctonia and Sclerotium were found associated with root rot. At seedling stage, the mean incidence of Rhizoctonia was the maximum (19.25%) followed by Fusarium (15.63%) and Sclerotium (4.63%) root rot. In low plastic tunnels, the overall incidence of Fusarium was the maximum (15.98%) followed by Rhizoctonia (14.1%) and Sclerotium (7.38%) root rot. At maturity stage in greenhouses, the incidence of Fusarium was the maximum (9.25%) followed by Rhizoctonia (6.22%) and Sclerotium (4.94%) root rot. However, in open fields, the incidence of Sclerotium was the maximum (14.35%) followed by Fusarium (8.31%) and Rhizoctonia (6.15%) root rot. Analysis of fruit and root rot samples employing morphological characterization, showed prevalence of 8 fungal species (Colletotrichum truncatum, Fusarium incarnatum, Fusarium proliferatum, Botrytis cinerea, Alternaria alternata, Fusarium equiseti, Rhizoctonia solani and Sclerotium rolfsii) belonging to 6 genera. Phylogenetic analysis showed the genetic homology of the subject isolates with previously submitted isolates in GenBank, confirming the morphological characterization. Highly virulent isolates of the most prevalent pathogen from fruit (C. truncatum isolate ACT12) and root (F. equiseti isolate FJH15) established during the pathogenicity test were selected for in vitro bio-control trials. Among natural compounds, chitosan was found the most effective with 55.55% radial mycelial growth inhibition at 2.5% concentration followed by salicylic acid (53.33%) and calcium chloride (27.77%). All the tested volatiles completely inhibited the radial mycelial growth at 100 ppm. Out of three Trichoderma species, T. harzianum was found the most effective with the maximum percent RMGI of 56.1%, followed by T. viride (53.5%) and T. hamatum (48.7%). The present study documents the fruit and root rot pathogens in Pothohar Plateau, Punjab, Pakistan. The morpho-molecular characterization further identifies pathogens up to specie level. The exploration of bio-control strategies in vitro will help to develop effective management under field conditions.