Fusarium fruit rot of bell pepper was found prevalent 100% in all the visited greenhouses and open fields during the month of February (greenhouses) and May (open fields) 2016-2017 in Attock, 10.5% to 18.3% with the average 13.63%. However, the disease incidence in open fields varied from 7.3% to 15% with the average of 12.04%. Standard protocol was followed for the isolation of pathogen from symptomatic fruit samples collected from the study area. Single-spore isolation technique was employed for obtaining pure culture of each Fusarium isolates. Based on morphological characteristics viz. colony color and appearance, phialides, and shapes and dimensions of conidia (micro-conidia, meso-conidia, macro-conidia and chlamydospores), twenty-nine isolates (72.5%) were confirmed as Fusarium incarnatum, whereas the remaining 11 isolates (27.5%) were confirmed as Fusarium proliferatum. Pathogenic nature of all the isolates was evaluated on the artificially inoculated bell pepper fruit following 0–5disease rating scale and percent disease severity index (DSI). All the isolates were able to cause disease symptoms, however10 isolates with 93-100% DSI were ranked as highly virulent. Translation elongation factor (EF-1α) gene of these isolates belonging to both species was sequenced, submitted to GenBank (for accession numbers) and grouped into separate clades (F. incarnatum and F. proliferatum) employing Mega7 software.