Anisakiasis, caused by nematodes from the Anisakidae family, has become a notable global health issue, primarily due to the increased consumption of raw or undercooked seafood. This study investigated the occurrence and prevalence of Anisakis larvae in commonly sold fish in Egyptian markets. Morphological and molecular techniques were employed to identify the larvae. Our findings revealed a high prevalence of Anisakis larvae, with 85% of Atlantic herring (Clupea harengus) and 52% of Atlantic mackerel (Scomber scombrus) being infected. The mean intensity of infection was 11.17 larvae per infected herring and 4.03 larvae per infected mackerel, while the mean abundance was 9.5 larvae per herring and 2.1 larvae per mackerel. Detailed morphological analysis identified the larvae as Anisakis simplex type I, characterized by specific anatomical features visible under light and scanning electron microscopy. DNA sequencing of the Internal Transcribed Spacer (ITS) region was aligned with GenBank data, confirming the identity of the larvae as A. simplex. This study highlights the significant presence of Anisakis larvae in the Egyptian fish supply, emphasizing the need for public health interventions to mitigate the risks associated with consuming raw or undercooked fish. The application of molecular techniques has enhanced our understanding of the species composition and potential health impacts of Anisakis in Egypt, contributing to global efforts to manage anisakiasis.