This study investigated the prevalence, molecular typing, as well as histopathological changes associated with Gotocotyla secundus infection in Scomberomorous commerson collected from Suez Governorate, Egypt. Identification of G. secundus was performed microscopically and genetically using C-PCR assay. Moreover, the phylogenetic tree was performed with MEGA X software analysis based on sequence analyses of the 28S rRNA gene using both neighbor–joining (NJ) and maximum-likelihood (ML) methods. The prevalence, abundance, and intensities of the parasite were calculated based on their collintary relationship with fish length and weight. Herein, G. secundus was mainly isolated from the gills and pseudobranchs of infested fish. Mostly, naturally infected fish have no pathognomonic lesions, except for a few cases that showed marbling of the gills. Histopathological studies revealed necrosis and fibrosis of the gill filaments with severe inflammatory reactions represented by the presence of lymphocytes and numerous giant cells.