The pathogenic Fusarium oxysporum species complex (FOSC) causes significant yield losses in the family Solanaceae including on tomato, eggplant and pepper in the Aegean and Mediterranean regions of Turkey. Fusarium wilt of pepper, caused by Fusarium oxysporum f. sp. capsici (Foc), has emerged recently in Turkey, where its significance has not been investigated thoroughly. In the present study, disease prevalence was determined with surveys conducted in 67 pepper-growing greenhouses and 56 pepper fields in the Aegean and Mediterranean regions in 2015 and 2016. In both years, about 32% of the greenhouses and 55% of the fields were found to be infested with the wilting disease. It was observed in a pathogenicity experiment that 64 isolates were pathogenic to pepper. In cross-inoculation experiments, these isolates did not cause wilting symptoms on tomato and eggplant and therefore were designated as Foc. Phylogenetic analyses were carried out with TEF-1 alpha and actA DNA regions of a selected subset of 40 Foc isolates, along with non-host formae of F. oxysporum and outgroup Fusarium species. Sequence data for the TEF-1 alpha and actA DNA regions displayed limited variation among Foc isolates and failed to distinguish reliably several formae speciales of F. oxysporum. The phylogenetic tree successfully separated the outgroup isolates. All Foc isolates were placed in the same branch, suggesting a single monophyletic group in the dendrogram. This is the first comprehensive study for pathogenic and phylogenetic analysis of Foc isolates from peppers in Turkey.