Worldwide, fish oil is an important and rich source of the health-beneficial omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA). It is, however, troubled by its high susceptibility towards lipid oxidation. This can be prevented by the addition of (preferably natural) antioxidants. The current research investigates the potential of Phaeodactylum carotenoids in this regard. The oxidative stability of fish oil and fish oil with Phaeodactylum addition is evaluated by analyzing both primary (PV) and secondary (volatiles) oxidation products in an accelerated storage experiment (37 °C). A first experimental set-up shows that the addition of 2.5% (w/w) Phaeodactylum biomass is not capable of inhibiting oxidation. Although carotenoids from the Phaeodactylum biomass are measured in the fish oil phase, their presence does not suffice. In a second, more elucidating experimental set-up, fish oil is mixed in different proportions with a Phaeodactylum total lipid extract, and oxidative stability is again evaluated. It was shown that the amount of carotenoids relative to the n-3 LC-PUFA content determined oxidative stability. Systems with a fucoxanthin/n-3 LC-PUFA ratio ≥ 0.101 shows extreme oxidative stability, while systems with a fucoxanthin/n-3 LC-PUFA ratio ≤ 0.0078 are extremely oxidatively unstable. This explains why the Phaeodactylum biomass addition did not induce oxidative stability.