Nutritionally they're the same, but they taste different. I add freshly ground flax seeds to my smoothies & cereals, to get he omega oils in my diet. For years I used brown, because that was the only seed offered locally. I added it to my meals because it was good for me, but found the flavor neutral - it didn't add or detract from a dish. Then a few years ago, my local health food store started selling the golden flax. I tried it & was surprised to find that it tasted nutty, buttery, and slightly sweet. Suddenly my smoothies & cereals tasted better. I've been using golden flax ever since. I find that if I buy it in the bulk section of the store, the price is still very reasonable.

According to a Canadian grower's association, there is no nutritional difference. I grind flax for fresh flax meal, and I can't tell the difference between brown and golden. There are people who believe there is a functional advantage in the golden but that seems to come from opinion, unsubstantiated by fact. The golden seems to have some kind of cachet that justifies the sometimes higher price. When I sold them (health food retailer for 29 years), the wholesale price was the same for them both.