Krill oil and salmon oil deliver the same core benefit, omega-3 fatty acids, but they differ in how your body absorbs those fats, how they taste going down, and what else comes in the capsule. Neither is categorically better. The right choice depends on what you’re taking it for, how sensitive your stomach is, and how much you’re willing to spend.
The Key Difference: How Omega-3s Are Packaged
Salmon oil delivers its omega-3s (EPA and DHA) attached to triglycerides, the same fat structure found in food. Krill oil delivers a significant portion of its omega-3s attached to phospholipids, a type of fat that forms cell membranes. This distinction matters because phospholipids mix with water more easily than triglycerides do, which means krill oil disperses in your stomach rather than sitting on top of digestive fluids like an oil slick.
Several studies have found that this phospholipid form leads to comparable or slightly better absorption of omega-3s at lower doses. In practical terms, a smaller krill oil capsule can deliver a similar amount of usable EPA and DHA as a larger salmon oil capsule. That said, the total omega-3 content per capsule is typically higher in salmon oil, so if you’re trying to hit a specific daily intake, you may need fewer salmon oil capsules to get there.
Joint Pain and Inflammation
Both krill oil and salmon oil have anti-inflammatory properties tied to their omega-3 content, but krill oil has been studied specifically for mild knee pain. A randomized controlled trial published in PLOS ONE found that krill oil significantly reduced pain and stiffness in people with mild knee joint issues compared to placebo. Participants reported less nighttime pain and less discomfort when standing, with statistically significant improvements on both measures.
That study did not find a significant drop in C-reactive protein (a blood marker of systemic inflammation), likely because participants didn’t have elevated inflammation levels to begin with. And when it comes to direct head-to-head comparisons with fish oil, the evidence is less dramatic. One earlier study on women with PMS-related knee pain found that 2 grams per day of krill oil improved symptoms, but the difference compared to the same dose of fish oil was not statistically significant. So while krill oil clearly helps with joint discomfort, it hasn’t been proven to outperform fish oil for that purpose.
Astaxanthin: Krill Oil’s Extra Ingredient
Krill oil naturally contains astaxanthin, the pigment that gives krill (and flamingos) their pink-red color. Astaxanthin is a potent antioxidant that protects the oil itself from going rancid and may offer additional benefits inside your body, including protecting cells from oxidative stress. Salmon oil doesn’t contain meaningful amounts of astaxanthin unless it’s been added during manufacturing.
This built-in antioxidant gives krill oil a longer shelf life without requiring as many added preservatives. It also means you’re getting a mild antioxidant boost with each dose, though the amount in a typical krill oil capsule is small compared to a standalone astaxanthin supplement.
Contaminants and Purity
Krill sit near the bottom of the food chain, feeding on phytoplankton in Antarctic waters. This gives krill oil a natural advantage when it comes to mercury contamination. An analysis of 11 commercial krill oil brands found mercury levels ranging from undetectable to just 0.041 mg/kg, which is extremely low. Salmon, being a larger predatory fish, accumulates more mercury over its lifetime, and salmon oil can carry trace amounts of that burden.
That said, krill oil isn’t completely clean. The same analysis found that lead levels were notably high across all krill oil samples tested, ranging from 0.157 to 0.435 mg/kg. This is a less commonly discussed concern but worth knowing. Quality salmon oil from reputable brands typically goes through molecular distillation, a purification process that strips out most heavy metals and environmental pollutants. So “lower on the food chain” doesn’t automatically mean purer in every respect. Brand quality and third-party testing matter more than the source animal.
Stomach Comfort and Fishy Burps
One of the most common reasons people switch to krill oil is the notorious “fish burp” problem. Because krill oil’s phospholipids emulsify in stomach fluid rather than floating on top, it’s less likely to cause that oily reflux sensation. Krill oil manufacturers market this as a key advantage, and many users confirm the difference.
However, krill oil can still cause fishy aftertaste and belching in some people. If you’re highly sensitive to fish oil supplements, krill oil will likely be gentler on your stomach, but it’s not a guarantee. Taking any omega-3 supplement with a meal that contains some fat reduces the chance of digestive discomfort regardless of the source.
Cost Per Gram of Omega-3
Krill oil is consistently more expensive than salmon oil, often two to three times the price per milligram of EPA and DHA. A standard krill oil capsule contains around 50 to 100 mg of combined EPA and DHA, while a salmon oil capsule typically delivers 300 to 500 mg. You’ll need more krill oil capsules to match the raw omega-3 content of salmon oil, which compounds the cost difference.
The phospholipid absorption advantage narrows this gap somewhat, since you may not need as high a dose of krill oil to achieve similar blood levels of omega-3s. But if budget is a factor and you tolerate fish oil well, salmon oil delivers more omega-3 per dollar.
Sustainability
Antarctic krill harvesting is regulated by the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR), which sets precautionary catch limits. The main fishing zone has a trigger level capped at 620,000 tons per year, with additional limits in other subareas. CCAMLR’s mandate explicitly requires that harvesting be sustainable and account for effects on the broader ecosystem, since krill are a critical food source for whales, seals, and penguins.
Wild salmon fisheries face their own sustainability pressures, particularly in the Pacific Northwest where some populations are endangered. Farmed salmon, which supplies much of the salmon oil market, raises separate concerns around habitat impact and feed sourcing. Neither option is free of ecological tradeoffs, but both have regulatory frameworks in place. If sustainability matters to you, look for certifications like the Marine Stewardship Council (MSC) label on either product.
Which One Should You Choose
Choose krill oil if you want a smaller capsule, less chance of fishy burps, a built-in antioxidant, and you’re willing to pay more. It’s a solid option for general omega-3 supplementation and mild joint support, especially if fish oil has bothered your stomach in the past.
Choose salmon oil if you want a higher omega-3 dose per capsule at a lower price and you don’t mind larger softgels. Salmon oil is a well-established, effective way to get EPA and DHA, and high-quality brands that use molecular distillation address most contamination concerns. For people aiming to support heart health or hit higher daily omega-3 targets recommended by their healthcare provider, salmon oil’s higher concentration per capsule makes it more practical.
Both oils raise your blood levels of omega-3 fatty acids. The differences are real but modest. Your consistency in taking them matters more than which one you pick.