Anisakidosis is a zoonotic infection caused by members of the family Anisakidae. The presence of anisakid larvae in fish poses risk for humans and dissuade consumers from purchasing infected products. Although fish constitute important component of Egyptian diet, the prevalence of anisakid larvae in marketed fish in Egypt is not well described. Furthermore, the species of anisakid larvae is not defined in most of the available studies due to the over reliance on morphological analyses. The aim of the current work was to assess the prevalence and intensity of anisakid larvae in three common marketed fish in Egypt (Atlantic herring, Mediterranean horse mackerel and Atlantic mackerel) and to determine the species of the isolated larvae using morphological and molecular methods. Light and scanning electron microscope (SEM) analyses revealed the details of the isolated larvae. However, partial sequencing of cytochrome oxidase subunite-1 (mt cox1) gene revealed that all larvae isolated from Atlantic herring and Mediterranean horse mackerel belonged to Anisakis simplex sensu stricto with prevalence of 87.1% and 83.3%, respectively, whereas Atlantic mackerel harbored Anisakis typica with a prevalence of 42.8%. The Mediterranean horse mackerel demonstrated the highest larval mean intensity (n = 20 larvae/infected fish). This study highlights the importance of these fish as potential reservoirs for human anisakiasis in Egypt and possibly in other coastal countries.