Fish oil comes from the tissue of oily, cold-water fish like anchovies, sardines, mackerel, herring, and menhaden. But the omega-3 fats inside those fish don’t actually originate in the fish themselves. They trace back to microscopic marine algae, the true starting point of every fish oil capsule on your shelf.
The Real Origin: Phytoplankton
Marine phytoplankton and single-cell algae are the primary producers of the omega-3 fatty acids EPA and DHA. These tiny organisms form the base of the ocean food web. Small fish like anchovies eat phytoplankton directly, accumulating omega-3s in their body fat. Larger predatory fish then eat those smaller fish, concentrating the fats further at each step up the chain. By the time you reach a salmon or tuna, the omega-3 content in their tissue reflects an entire food web’s worth of accumulation. In essence, phytoplankton are the origin of the majority of the omega-3s humans consume.
Which Fish Are Used
Most commercial fish oil comes from small, oily species caught in large volumes: anchovies, sardines, mackerel, herring, and menhaden. These species are favored because they’re abundant, rich in body fat, and sit low enough on the food chain that they carry fewer environmental contaminants than larger predators. A growing share of fish oil also comes from processing byproducts of farmed fish. Tuna trimmings, for example, yield refined oils where polyunsaturated fats make up over 40% of the total, with about 30% consisting of EPA and DHA combined.
This use of byproducts, including heads, frames, and viscera from fish processed for food, has become an important supplement to whole-fish sourcing. It reduces waste and eases pressure on wild fish stocks dedicated solely to oil production.
Body Oil vs. Liver Oil
There’s an important distinction between standard fish oil and cod liver oil, even though both end up in similar-looking capsules. Standard fish oil is extracted from the whole body of the fish and provides EPA and DHA with only trace amounts of vitamins. Cod liver oil, as the name suggests, comes specifically from the liver of cod. Because vitamin D concentrates in the liver, cod liver oil is a rich source of both vitamin D and vitamin A alongside its omega-3 content.
This difference matters if you’re taking fish oil for a specific reason. Someone looking purely for omega-3s would choose standard fish oil. Someone looking to address a vitamin D shortfall might prefer cod liver oil, though the added vitamin A means higher doses require more caution.
How Fish Oil Is Extracted and Purified
Raw fish oil starts as a crude product separated from the fish through cooking, pressing, and centrifuging. At this stage, the oil contains not just omega-3 fatty acids but also environmental contaminants like dioxins, PCBs, and trace heavy metals that the fish absorbed during their lives.
Removing those contaminants is one of the most critical steps in production. The industry standard is a process called short-path distillation (sometimes called molecular distillation). It works by heating the oil under a high vacuum with only a short distance between the heating surface and a cooling surface. Molecules of different weights evaporate at different rates, allowing the desirable fatty acids to be separated from the pollutants. Commercial-scale processing using this method removes 76% to 99% of dioxins, PCBs, and related persistent organic pollutants, with higher temperatures producing the cleanest results. Some producers add a small percentage of a volatile working fluid to improve decontamination at lower temperatures, which helps preserve the oil’s quality during processing.
After distillation, the oil undergoes further refining steps to reduce off-flavors and oxidation. The industry group GOED sets voluntary quality limits that most reputable manufacturers follow: a peroxide value below 5 (measuring early-stage oxidation), an anisidine value below 20 (measuring later-stage oxidation), and a combined total oxidation score below 26. These numbers essentially measure how “fresh” the oil is, since omega-3 fats are fragile and break down when exposed to heat, light, or air.
Algae-Based Alternatives
Since phytoplankton are the original source of omega-3s, it’s possible to skip the fish entirely. Algal oil is produced by growing specific strains of microalgae in controlled tanks called photobioreactors. The algae are fed nutrients (primarily nitrogen and phosphorus), water, CO2, and artificial light, often from LEDs, which research has shown to be more effective than sunlight for this purpose.
To maximize omega-3 production, growers manipulate the growth conditions. When nitrogen in the culture runs low relative to the carbon supply, the algae shift their metabolism toward storing lipids, including DHA. The resulting oil is extracted, refined, and sold as a vegan omega-3 supplement. It provides DHA and, depending on the algal strain, varying amounts of EPA. The process is more expensive than traditional fish oil production due to the cost of the bioreactors and controlled lighting, which is why algal oil supplements typically carry a higher price tag. But for people who avoid animal products or are concerned about ocean sustainability, it offers the same fundamental nutrient traced back to its true biological source.