Capillaria philippinensis larva is a nematode parasite causing intestinal capillariasis, a fish-borne disease that has become more prevalent in the recent years. The present study aimed to investigate the prevalence of Capillaria philippinensis in some fresh water fish in El-Minya Governorate. A total of 110 fish samples [56 wild bajad (Bagrus bajad) and 54 farmed carp fish (Cyprinus carpio)] were randomly collected from markets and some fish farms in El-Minya Governorate. In intestinal survey of examined fish, adult nematodes, larvae and high number of free eggs were observed only in intestine of Bagrus bajad, at infection rate of 58.93% (33/56).Regarding morphological characteristics of the detected adult nematodes and their eggs, they were identified as Capillaria spp. The total infection rate of Capillaria spp. in examined fish samples was 30% (33/110). Molecular identification of 25 Capillarid samples isolated from examined fish using recycling PCR technique included sequences and phylogenetic analysis of the Nematode 18S rDNA gene fragment. Confirmed identification of the detected species as Capillaria  philippinensis larvae based on the similarity of nucleotide sequences and phylogenetic relationships. In conclusion, this work indicated high prevalence rate of Capillaria spp. in wild Bagrus bajad in El-Minya Governorate. Morphological examination of the detected parasite and molecular analysis identified  Capillaria philippinensis larvae.