This research investigates the prevalence and mean intensity of Anisakis larvae on the bigeye scad, Selar crumenophthalmus (Bloch, 1793), along the Indian Ocean off Java. In total, 498 fish samples were collected from four locations: the Indian Ocean off East Java, Yogyakarta Special Territory, Central Java, and West Java. Each fish sample was measured for length and weight, then examined for Anisakis larvae in the abdominal cavity, liver, gonads, digestive tract, and muscle. Morphological characterisation was done using scanning electron microscope (SEM). The ITS rDNA region was amplified using PCR, then used to perform RFLP for identification and sequenced to form a phylogenetic tree. The results demonstrated that the bigeye scad was vulnerable to infection by Anisakis nematodes with varying prevalence and mean intensity at each location. The bigeye scad from the Indian Ocean off East Java had the highest prevalence and mean intensity (P = 75.44 %; MI = 10.38 larvae per-host), while from West Java had the lowest prevalence (P = 1.45 %; MI = 3.33 larvae per-host). The prevalence of Anisakis in the bigeye scad tends to decrease as one moves to the west from the sampling locations. Most larvae were found in the abdominal cavity (70 %–100 %), whereas a relatively low prevalence was found in other organs. The direct sequencing in the ITS rDNA region showed that Anisakis larvae found in the bigeye scad were A. typica (Diesing, 1860), which was indicated as A. typica var. indonesiensis (A. typica sp. B). Anisakis infection can be utilised as a biological indicator for movement patterns and fish stock differentiation.